LAMP Constructs

ABSTRACT

The present invention provides improved LAMP Constructs comprising specific fragments of the LAMP lumenal domain to deliver antigens to immune cells for enhanced processing. These LAMP Constructs can be used for the treatment of disease and in particular, allergies, infectious disease, diabetes, hyperproliferative disorders and/or cancer. The improved LAMP Constructs allow for presentation of properly configured three dimensional epitopes for production of an immune response when administered to a subject. The improved LAMP Constructs can be multivalent molecules, and/or can be provided as part of a multivalent vaccine containing two or more LAMP Constructs. The improved LAMP Constructs as described herein can also be used to generate antibodies when administered to a non-human vertebrate.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.16/607,082, filed Oct. 21, 2019, which is a national stage applicationof International Patent Application No. PCT/US2018/028753, filed Apr.22, 2018, which claims priority to U.S. Provisional Application Nos.62/549,033 filed Aug. 23, 2017, 62/549,119, filed Aug. 23, 2017, and62/488,741, filed Apr. 22, 2017, each of which is incorporated in theirentirety by reference herein.

BACKGROUND OF THE INVENTION Field of the Invention

The invention relates to improved LAMP Constructs and their use intreating subjects suffering from infectious disease, diabetes,allergies, hyperproliferative disorders and/or cancer. Additionally,improved LAMP constructs described herein can be used to generateantibodies in non-human vertebrates preferably where the genome of thenon-human vertebrates comprise at least partially human immunoglobulinregions and/or humanized immunoglobulin regions. Prime boost protocolsutilizing the LAMP improved Constructs described herein are alsodescribed.

Discussion of the Related Art

In the following discussion, certain articles and methods will bedescribed for background and introductory purposes. Nothing containedherein is to be construed as an “admission” of prior art. Applicantexpressly reserves the right to demonstrate, where appropriate, that thearticles and methods referenced herein do not constitute prior art underthe applicable statutory provisions.

DNA vaccines are new and promising candidates for the development ofboth prophylactic and therapeutic vaccines. They are proven to be safeand the lack of immune responses to a vector backbone may be adefinitive advantage if repetitive cycles of vaccination are required toachieve clinical benefits. However, one perceived disadvantage ofconventional DNA vaccines is their low immunogenicity in humans. A keylimiting step in the immunogenicity of epitope-based DNA vaccines may bethe access of epitopes to the MHCII presentation pathway to T cells,which is likely a stochastic process in the case of a vaccine withouttargeting technology.

U.S. Pat. No. 5,633,234 describes chimeric proteins comprising anantigenic domain of modified influenza hemagglutinin (HA) and acytoplasmic endosomal/lysosomal targeting signal which effectivelytarget antigens to that compartment. The antigenic domain was processedand peptides from it presented on the cell surface in association withmajor histocompatibility (MHC) class II molecules. The cytoplasmic tailof LAMP-1 was used to form the endosomal/lysosomal targeting domain ofthe chimeric protein.

U.S. Pat. No. 8,318,173 extended these initial observations to describechimeric proteins (and the corresponding DNAs that encode theseproteins) comprising the HIV-1 Gag protein inserted between the fulllumenal domain and a transmembrane domain of LAMP-1. This construct wasintroduced into dendritic cells which were then reported to target theMHC II pathway.

This approach has proved useful in increasing cellular and humoralresponses to several virus antigens, human papillomavirus E7, denguevirus membrane protein, HIV-1 gp160 membrane protein, HIV-1 P55 Gag,West Nile membrane protein, hepatitis C virus NS3 protein andcytomegalovirus pp65 (see, e.g., Bonini, et al., J. Immunol. 166:5250-5257, 2001). The enhanced immune response can be attributed toco-localization of LAMP with MHC II and the more efficient processingand delivery of antigenic peptides. In addition, LAMP-targeting isreported to result in the presentation of an increased number ofimmunogenic epitopes, thus inducing a qualitatively broadened immuneresponse compared to untargeted antigen. For example, Fernandes et al.,2000, Eur. J. Immunol. 30(8): 2333-43, demonstrated an increase in thenumber of presented peptides of a LAMP-trafficked OVA antigen encoded ina vaccinia vector. Of 12 peptides generated from exogenously suppliedOVA, 9 were presented by an OVA/LAMP chimera, as compared to only 2 bythe construct without LAMP.

While it has been determined that the cytoplasmic domain of LAMP isnecessary (in conjunction with a signal sequence and transmembranedomain), it is not always sufficient for endosomal/lysosomal traffickingof all antigens. Instead, the full lumenal domain of LAMP has been shownto be also required for the trafficking of proteins to the lysosomalvesicular pathway.

However, even with the presence of the complete lumenal domain and thecomplete transmembrane/cytoplasmic tail of LAMP (“complete LAMPConstructs”), it has increasingly been found that the efficacy of aparticular antigen to raise an immune response is highly dependent onthe particular sequence used in these constructs. In fact, differentantigenic fragments of the same protein when inserted into the completeLAMP constructs have been found to not elicit the same immune response.Sometimes the antigen fragment generates an immune response and othertimes it does not. These observations make the ability to predict aheadof time which particular antigenic sequence from a protein of interestwill raise an immune response difficult with the complete LAMPConstructs.

Moreover, in generating the complete LAMP Constructs, it has beenrepeatedly observed that the full lumenal domain is required to properlyexpress and process an antigen. For example, in Godinho et al., PLoS ONE9(6): 9(6): e99887. doi:10.1371/journal.pone.0099887, the authorsreported that the complete and intact lumenal domain was the necessaryminimal region needed to target an antigen to the lysosomes and thatfragments of the lumenal domain did not work. See, id. at page 6.

Specifically, the Godinho authors showed that by completely removing thefirst luminal domain and some of the second luminal domain (i.e.,T1-Lum/gag construct), both protein expression and antibody response isdecreased. Similarly, removing 25% of first luminal domain but having anintact second luminal domain (i.e., T2-lum/gag), both protein expressionand antibody response comparatively increased but still less than theresults obtained with the complete LAMP construct.

Moreover, the authors acknowledged that the ability to raise an immuneresponse is dependent upon the particular antigen and the epitopes usedin these complete LAMP Constructs. For example, on page 9, column 2, theauthors state “accordingly, previous studies demonstrated that DNAvaccines that generate Gag secreted as VLP, or in a soluble form, inducedifferent levels of T and B cell activation, which were also differentfrom the response induced by cytoplasmic Gag.” However, insertion of anantigenic sequence between the full lumenal domain of LAMP and the fulltransmembrane/cytoplasmic domain of LAMP as has been described in theliterature results in such large polynucleotide sequences that itbecomes either too costly to produce at commercial levels or impracticalfrom a scientific perspective.

Thus, there is a need to design new and improved LAMP Constructs thatcan be used as vaccines to effectively treat, for example, allergies,infectious disease, diabetes, hyperproliferative disorders and/orcancer. Moreover, once improved, these new LAMP Constructs can be usedto generate antibodies.

SUMMARY OF THE INVENTION

This Summary is provided to introduce a selection of concepts in asimplified form that are further described below in the DetailedDescription. This Summary is not intended to identify key or essentialfeatures of the claimed subject matter, nor is it intended to be used tolimit the scope of the claimed subject matter. Other features, details,utilities, and advantages of the claimed subject matter will be apparentfrom the following written Detailed Description including those aspectsillustrated in the accompanying drawings and defined in the appendedclaims.

It is an object of this invention to provide novel constructs (“improvedLAMP Constructs”) comprising specific fragments and/or variants of LAMPdomains that effectively present an antigen(s) of interest to the immunesystem to generate an enhanced immune response. These improved LAMPConstructs effectively direct the antigens to the lysosomal/endosomalcompartment where they are processed and presented to majorhistocompatibility complex (MHC) class II molecules so that helper Tcells are preferentially stimulated and/or antibodies are generated.

The improved LAMP Constructs and methods described herein may elicit animmune response in a subject. The immune response may be an immuneresponse to the epitopes of the antigens in the improved LAMP Construct(e.g., vaccine). Vaccines arm the immune system of the subject such thatthe immune system may detect and destroy that which contains theantigens of the vaccines in the subject. The improved LAMP Constructsand methods described herein may elicit a Thl immune response in thesubject. Thl immune responses may include secretion of inflammatorycytokines (e.g., IFNγ, TNFa) by a subset of immune cells (e.g., antigenspecific T-cells). In some cases, the inflammatory cytokines activateanother subtype of immune cells (e.g., cytotoxic T-cells) which maydestroy that which contains the antigen in the subject.

In some cases, the epitopes and/or antigens used in the improved LAMPConstructs and methods described herein may be recognized by the immunesystem of a subject to elicit a Thl immune response and release Type Icytokines. The Thl response may be initiated by the interaction betweenthe epitope and the T-cell, more specifically, the majorhistocompatibility complex (MHC) expressed by the T-cell. For example,high affinity binding of an epitope to an MHC receptor may stimulate aThl response. MHC receptors may be at least one of a plurality of typesof MHC receptors. The MHC receptors engaged on a T-cell may vary acrossindividuals in a population.

In some cases, the immune response is a Type 1 immune response. In somecases, the immune response is characterized by a ratio of Type Icytokine production to Type II cytokine production that is greaterthan 1. In some cases, the immune response is characterized by a ratioof Type I cytokine production to Type II cytokine production that isless than 1. In some cases, the immune response is characterized by aratio of IFNy production to IL-10 production that is greater than 1. Insome cases, the immune response is characterized by a ratio of IFNyproduction to IL-10 production that is less than 1.

It is yet another object of this invention to provide improved methodsof treatment for cancer and/or hyperproliferative disorders by elicitingan anti-tumor immune response through stimulation of helper T cells.

The improved LAMP Constructs described herein can also be used to treatallergies, such as for example, food allergies (e.g., peanut allergens,such as Ara H1, H2 and/or H3), or environmental allergens, such as forexample pollen (tree pollen, such as for example CRY J1 or CRY J2), dogdander, cat saliva, or dust mites. Oiher diseases and/or disorders thatcan be treated using the improved LAMP Constructs described hereininclude, for example, infectious disease and diabetes.

The invention further provides a nucleic acid molecule encoding any ofthe improved LAMP Constructs described herein. The invention alsoprovides an improved LAMP Construct comprising an antigen to generateantibodies. The improved LAMP Construct can comprise a nucleic acidwherein the nucleic acid molecule is operably linked to an expressioncontrol sequence. In one preferred aspect, the improved LAMP Constructis a vaccine vector, suitable for vaccinating a patient. In anotheraspect, the invention provides a delivery vehicle comprising theimproved LAMP Construct for facilitating the introduction of the nucleicacid molecule encoding the antigen into a cell. The delivery vehicle maybe lipid-based (e.g., a liposome formulation), viral-based (e.g.,comprising viral proteins encapsulating the nucleic acid molecule), orcell-based.

In preferred embodiments, the invention provides an injectablecomposition comprising an improved LAMP Construct comprising an antigenof interest for eliciting an immune response (e.g., generation ofantibodies) in a mammal to an antigen. In preferred embodiments, thisvaccine generates a preferential Th1 response to a Th2 response. Theimproved LAMP Constructs comprise at least one epitope of an antigen.

The invention also provides a cell comprising any of the improved LAMPConstructs described herein which can be used to generate an immuneresponse. In one aspect, the cell is an antigen presenting cell. Theantigen presenting cell may be a professional antigen presenting cell(e.g., a dendritic cell, macrophage, B cell, and the like) or anengineered antigen presenting cell (e.g., a non-professional antigenpresenting cell engineered to express molecules required for antigenpresentation, such as MHC class II molecules). The molecules requiredfor antigen presentation may be derived from other cells, e.g.,naturally occurring, or may themselves be engineered (e.g. mutated ormodified to express desired properties, such as higher or lower affinityfor an antigenic epitope). In one aspect, the antigen presenting celldoes not express any co-stimulatory signals and the antigen is anauto-antigen.

The invention additionally provides a kit comprising a plurality ofcells comprising any of the improved LAMP Constructs described herein.At least two of the cells express different MHC class II molecules, andeach cell comprises the same LAMP Construct. In one aspect, a kit isprovided comprising an improved LAMP Construct and a cell for receivingthe vector.

The invention also provides a transgenic animal comprising at least oneof the cells and/or at least one of the improved LAMP Constructsdescribed herein. The invention also provides a transgenic animalcomprising at least one of the cells described herein.

The invention further provides a method for generating an immuneresponse in an animal (e.g., a human or a non-human vertebrate) to anantigen, comprising: administering to the animal a cell as describedabove, wherein the cell expresses, or can be induced to express, theimproved LAMP Construct in the animal. In one aspect, the cell comprisesan MHC class II molecule compatible with MHC proteins of the animal,such that the animal does not generate an immune response against theMHC class II molecule. In one preferred aspect, the animal is a human.

In one further aspect, the invention provides a method for eliciting animmune response to an antigen, comprising administering to an animal,such as a human or a non-human vertebrate, any of the improved LAMPConstructs described herein. Preferably, the improved LAMP Construct isinfectious for a cell of the animal. For example, the improved LAMPConstruct may be a viral vector, such as a vaccinia improved LAMPConstruct.

Prime boost protocols are also contemplated. For example, the inventionfurther provides a method for generating an immune response in an animalto an antigen, comprising priming the animal with an improved LAMPConstruct comprising an antigen as described herein followed by at leastone boosting of the animal with the antigen or a related antigen (e.g.,a second antigen derived from the same or highly similar proteinsequence). Mixtures of antigens can be used in either or both thepriming and the boosting step. Use of an improved LAMP Construct for theprime step followed by an antigen boost step has been shown tosignificantly produce higher titers, indicating the power of LAMP inenhancing antibody response.

In a further aspect, a cell is obtained from a patient, the improvedLAMP Construct described herein is introduced into the cell and the cellor progeny of the cell is reintroduced into the patient. In one aspect,the cell is a stem cell-capable of differentiating into an antigenpresenting cell. Treatments of human patients as well as veterinary useare specifically contemplated.

The present invention also comprises methods of generating antibodies ina non-human vertebrate wherein the non-human vertebrate is injected withan improved LAMP Construct comprising an antigen of interest asdescribed herein. The antigen of interest is then efficiently presentedto the immune system with the help of LAMP in the non-human vertebrateto raise antibodies against the antigen.

Specifically, by combining presentation of the antigen of interest withLAMP, the antigen is then effectively transported to the cytoplasmicendosomal/lysosomal compartments, where the antigen can be processed andpeptides from it presented on the cell surface in association with majorhistocompatibility (MHC) class II molecules.

These generated antibodies can be isolated from the blood of thevertebrate (as polyclonals) and then further isolated to generatemonoclonal antibodies using standard techniques.

In preferred embodiments, the genome of the non-human vertebratecomprises an introduced partially human immunoglobulin region, saidintroduced region comprising human immunoglobulin variable region locuscoding sequences and non-coding sequences based on the endogenousimmunoglobulin variable region locus of the non-human vertebrate.Preferably, non-human vertebrate's genome has at least part or all ofthe endogenous immunoglobulin region removed.

In further preferred embodiments, the production of human monoclonalantibodies in the non-human vertebrate requires that the host have atleast one locus that will express human heavy chain immunoglobulinproteins and one locus that will express human light chainimmunoglobulin proteins.

In some aspects, the partially human immunoglobulin variable regionlocus comprises human V_(H) coding sequences and non-coding V_(H)sequences based on the endogenous V_(H) region of the non-humanvertebrate. In these aspects, the partially human immunoglobulinvariable region locus further comprises human D and J gene codingsequences and non-coding D and J gene sequences based on the endogenousgenome of the non-human vertebrate host.

In other aspects, the immunoglobulin region comprises an introducedregion comprising human V_(L) coding sequences and non-coding V_(L)sequences based on the endogenous V_(L) region of the non-humanvertebrate. More preferably, the introduced partially humanimmunoglobulin region comprising human V_(L) coding sequences furthercomprises human J gene coding sequences and non-coding J gene sequencesbased on the endogenous genome of the non-human vertebrate host.

In certain aspects, the vertebrate is a mammal, and preferably themammal is a rodent, e.g., a mouse or rat. In other aspects, thevertebrate is avian, e.g., a chicken. Other non-human vertebratesinclude rabbits, llamas, camels, a cow, a guinea pig, a hamster, a dog,a cat, a horse, a non-human primate, a simian (e.g. a monkey or ape), amonkey (e.g. marmoset, baboon, rhesus macaque), or an ape (e.g. gorilla,chimpanzee, orangutan, gibbon).

In further embodiments, the partially human immunoglobulin regioncomprises human V_(H) gene coding regions, and further comprises i)human D and J gene coding sequences and ii) non-coding D and J gene andpre-DJ sequences based on the endogenous genome of the non-humanvertebrate host. In other aspects, the V_(H) gene coding regions derive(at least partially) from other sources—e.g., they could be rationallyor otherwise designed sequences, sequences that are a combination ofhuman and other designed sequences, or sequences from other species,such as nonhuman primates.

In yet another specific aspect, the partially human immunoglobulinregion comprises human V_(L) gene coding regions, and further comprisesi) human J gene coding sequences and ii) non-coding J gene sequencesbased on the endogenous genome of the non-human vertebrate host. In aspecific aspect, the partially human immunoglobulin region compriseshuman V_(H) coding regions, human D and J gene coding sequences, andnon-coding D and J gene and pre-DJ sequences based on the endogenousgenome of the non-human vertebrate host.

The methods described herein can be used in the production and/oroptimization of antibodies, including fully human antibodies, humanizedantibodies, chimeric antibodies, for diagnostic and therapeutic uses.Hybridomas producing such antibodies are also a further object of theinvention.

These and other aspects, objects and features are described in moredetail below.

BRIEF DESCRIPTION OF THE FIGURES

The objects and features of the invention can be better understood withreference to the following detailed description and accompanyingdrawings.

FIG. 1 illustrates the general scheme of different types of improvedLAMP Constructs (identified as ILC-1, ILC-2, ILC-3, ILC-4, ILC-5 andILC-6) that can be used as described herein.

FIG. 2A illustrates the domains of the LAMP proteins defined hereinwhile FIG. 2B defines the specific amino acid boundaries of thesedomains for human LAMP-1 (SEQ ID NO:1), human LAMP-2 (SEQ ID NO:2),human LAMP-3 (SEQ ID NO:3), human LIMP-2 (SEQ ID NO:4), human Endolyn(SEQ ID NO:5), human Macrosailin (SEQ ID NO:80), human LAMP-5 (SEQ IDNO:93) and human LIMBIC (SEQ ID NO:67). As described herein the LAMPlumenal domains, homology domains, transmembrane domains, thecytoplasmic tail and the signal sequences can be used to generate theimproved LAMP Constructs ILC-1, ILC-2, ILC-3, ILC-4, ILC-5 and ILC-6 asdescribed herein.

FIG. 3 provides alignment of LAMP-1 proteins found in other species ascompared to human LAMP-1 (SEQ ID NO:1). The equivalent domains of theseother species can be used to generate the improved LAMP Constructsdescribed herein and are readily identifiable by comparing the domainsidentified for human LAMP-1 in FIG. 2 and FIG. 3 to the alignments shownin FIG. 3.

FIG. 4 provides alignment of LAMP-2 proteins found in other species ascompared to human LAMP-2 (SEQ ID NO:2). The equivalent domains of theseother species can be used to generate the improved LAMP Constructsdescribed herein and are readily identifiable by comparing the domainsidentified for human LAMP-2 in FIG. 2 and FIG. 4 to the alignments shownin FIG. 4.

FIG. 5 provides alignment of LAMP-3 proteins found in other species ascompared to human LAMP-3 (SEQ ID NO:3). The equivalent domains of theseother species can be used to generate the improved LAMP Constructsdescribed herein and are readily identifiable by comparing the domainsidentified for human LAMP-3 in FIG. 2 and FIG. 5 to the alignments shownin FIG. 5.

FIG. 6 provides alignment of LIMP-2 proteins found in other species ascompared to human LIMP-2 (SEQ ID NO:4). The equivalent domains of theseother species can be used to generate the improved LAMP Constructsdescribed herein and are readily identifiable by comparing the domainsidentified for human LIMP-2 in FIG. 2 and FIG. 6 to the alignments shownin FIG. 6.

FIG. 7 provides alignment of LIMBIC proteins found in other species ascompared to human LIMBIC (SEQ ID NO:67). The equivalent domains of theseother species can be used to generate the improved LAMP Constructsdescribed herein and are readily identifiable by comparing the domainsidentified for human LIMBIC in FIG. 2 and FIG. 7 to the alignments shownin FIG. 7.

FIG. 8 provides alignment of Endolyn proteins found in other species ascompared to human Endolyn (SEQ ID NO:5). The equivalent domains of theseother species can be used to generate the improved LAMP Constructsdescribed herein and are readily identifiable by comparing the domainsidentified for human Endolyn in FIG. 2 and FIG. 8 to the alignmentsshown in FIG. 8.

FIG. 9 provides alignment of Macrosailin proteins found in other speciesas compared to human Macrosailin (SEQ ID NO:80). The equivalent domainsof these other species can be used to generate the improved LAMPConstructs described herein and are readily identifiable by comparingthe domains identified for human Macrosailin in FIG. 2 and FIG. 9 to thealignments shown in FIG. 9.

FIG. 10 provides alignment of LAMP-5 proteins found in other species ascompared to human LAMP-5 (SEQ ID NO:93). The equivalent domains of theseother species can be used to generate the improved LAMP Constructsdescribed herein and are readily identifiable by comparing the domainsidentified for human LAMP-5 in FIG. 2 and FIG. 10 to the alignmentsshown in FIG. 10.

FIG. 11 shows results obtained when mice were immunized with HVEM-LAMP,HVEM, or LAMP on day 0, 7, and 14. On day 28, mice were bled and serumsamples were isolated. HVEM specific IgG was examined by ELISA. Datarepresent geometric mean of antibody titers±geometric SD, n=6. ** pvalue<0.01

FIG. 12 shows results obtained when mice were immunized with HVEM-LAMP,HVEM, or LAMP on day 0, 7, and 14. On day 35, mice were boosted with 5 gHVEM protein in the presence of alum adjuvant. Mice were bled on day 49and serum samples were isolated. HVEM specific IgG was examined byELISA. Data represent geometric mean of antibody titers±geometric SD,n=6. *** p value<0.001; **** p value<0.0001.

FIG. 13 shows that LAMP alters the binding affinity of epitopes inCRD3/4 of HVEM.

FIG. 14 confirms protein expression of tested improved LAMP Constructs.In each of FIGS. 14-17, the labels “complete LAMP Construct”, ILC-1,ILC-2, ILC-3 and ILC-4 correspond to the constructs as depicted in FIG.1.

FIG. 15 shows that the improved LAMP Constructs induce Th1 effector Tcells producing INFγ.

FIG. 16 shows a particular improved LAMP construct (e.g., ILC-4 as shownin FIG. 1) elicited a significantly higher T cell response against allsurvivin peptide pools.

FIG. 17 shows that CD4 T cells are the major source of IFNγ producingcells and that the improved LAMP Constructs demonstrate an increase inthe CD4 effector memory cell population over the Complete LAMPconstruct.

FIG. 18 shows that the improved LAMP Constructs produced strongerSurvivin-specific total IgG response in BALB/c mice.

FIG. 19 provides the amino acid sequence of each LAMP construct tested.The signal sequence of each construct is depicted as lower case andunderlined letters; the Survivin sequence is depicted in capitalized,white letters, shaded in black; the luminal domain is depicted initalics and capitalized letters and the transmembrane/cytolosolic domainis depicted in capitalized letter and shaded in grey, and in ILC-4, thesecond homology domain is bolded. Additional amino acids (LE and EF) maybe included as part of the cloning linkers.

DETAILED DESCRIPTION

The invention provides improved LAMP Constructs and nucleic acidsencoding these which can be used to generate vaccines and/or used toraise antibodies. The improved LAMP Constructs can be used to modulateor enhance an immune response. In one preferred aspect, the inventionprovides a method for treating a patient with an allergy, infectiousdisease, diabetes, cancer or a hyperproliferative disorder by providingan improved LAMP Construct described herein. The improved LAMPConstructs can also be used to raise antibodies in non-humanvertebrates, and in preferably, non-human mammals.

Definitions

The following definitions are provided for specific terms which are usedin the following written description.

As used in the specification and claims, the singular form “a”, “an” and“the” include plural references unless the context clearly dictatesotherwise. For example, the term “a cell” includes a plurality of cells,including mixtures thereof. The term “a nucleic acid molecule” includesa plurality of nucleic acid molecules.

As used herein, the term “comprising” is intended to mean that theimproved LAMP Constructs and methods include the recited elements, butdo not exclude other elements. “Consisting essentially of”, when used todefine improved LAMP Constructs and methods, shall mean excluding otherelements of any essential significance to the combination. Thus, animproved LAMP Construct consisting essentially of the elements asdefined herein would not exclude trace contaminants from the isolationand purification method and pharmaceutically acceptable carriers, suchas phosphate buffered saline, preservatives, and the like. “Consistingof” shall mean excluding more than trace elements of other ingredientsand substantial method steps for administering the improved LAMPConstructs of this invention. Embodiments defined by each of thesetransition terms are within the scope of this invention.

The term “about” or “approximately” means within an acceptable range forthe particular value as determined by one of ordinary skill in the art,which will depend in part on how the value is measured or determined,e.g., the limitations of the measurement system. For example, “about”can mean a range of up to 20%, preferably up to 10%, more preferably upto 5%, and more preferably still up to 1% of a given value.Alternatively, particularly with respect to biological systems orprocesses, the term can mean within an order of magnitude, preferablywithin 5 fold, and more preferably within 2 fold, of a value. Unlessotherwise stated, the term ‘about’ means within an acceptable errorrange for the particular value, such as +1-20%, preferably +1-10% andmore preferably ±1-5%.

Where a range of values is provided, it is understood that eachintervening value, between the upper and lower limit of that range andany other stated or intervening value in that stated range isencompassed within the invention. The upper and lower limits of thesesmaller ranges may independently be included in the smaller ranges, andare also encompassed within the invention, subject to any specificallyexcluded limit in the stated range. Where the stated range includes oneor both of the limits, ranges excluding either both of those includedlimits are also included in the invention.

As used herein, “the lysosomal/endosomal compartment” refers tomembrane-bound acidic vacuoles containing LAMP molecules in themembrane, hydrolytic enzymes that function in antigen processing, andMHC class II molecules for antigen recognition and presentation. Thiscompartment functions as a site for degradation of foreign materialsinternalized from the cell surface by any of a variety of mechanismsincluding endocytosis, phagocytosis and pinocytosis, and ofintracellular material delivered to this compartment by specializedautolytic phenomena (de Duve, Eur. J. Biochem. 137: 391, 1983). The term“endosome” as used herein and in the claims encompasses a lysosome.

As used herein, a “lysosome-related organelle” refers to any organellewhich comprises lysosymes and includes, but is not limited to, MIIC,CIIV, melanosomes, secretory granules, lytic granules, platelet-densegranules, basophil granules, Birbeck granules, phagolysosomes, secretorylysosomes, and the like. Preferably, such an organelle lacks mannose6-phosphate receptors and comprises LAMP, but may or may not comprise anMHC class II molecule. For reviews, see, e.g., Blott and Griffiths,Nature Reviews, Molecular Cell Biology, 2002; Dell'Angelica, et al., TheFASEB Journal 14: 1265-1278, 2000.

As used herein, the terms “polynucleotide” and “nucleic acid molecule”are used interchangeably to refer to polymeric forms of nucleotides ofany length. The polynucleotides may contain deoxyribonucleotides,ribonucleotides, and/or their analogs. Nucleotides may have anythree-dimensional structure, and may perform any function, known orunknown. The term “polynucleotide” includes, for example, single-,double-stranded and triple helical molecules, a gene or gene fragment,exons, introns, mRNA, tRNA, rRNA, ribozymes, antisense molecules, cDNA,recombinant polynucleotides, branched polynucleotides, aptamers,plasmids, vectors, isolated DNA of any sequence, isolated RNA of anysequence, nucleic acid probes, and primers. A nucleic acid molecule mayalso comprise modified nucleic acid molecules (e.g., comprising modifiedbases, sugars, and/or internucleotide linkers).

As used herein, the term “peptide” refers to a compound of two or moresubunit amino acids, amino acid analogs, or peptidomimetics. Thesubunits may be linked by peptide bonds or by other bonds (e.g., asesters, ethers, and the like).

As used herein, the term “amino acid” refers to either natural and/orunnatural or synthetic amino acids, including glycine and both D or Loptical isomers, and amino acid analogs and peptidomimetics. A peptideof three or more amino acids is commonly called an oligopeptide if thepeptide chain is short. If the peptide chain is long (e.g., greater thanabout 10 amino acids), the peptide is commonly called a polypeptide or aprotein. While the term “protein” encompasses the term “polypeptide”, a“polypeptide” may be a less than full-length protein.

As used herein a “LAMP polypeptide” refers to the mammalian lysosomalassociated membrane proteins human LAMP-1, human LAMP-2, human LAMP-3,human LIMP-2, human Endolyn, human LIMBIC, human LAMP-5, or humanMacrosailin as described herein, as well as orthologs (such as, forexample, the LAMP proteins shown in FIGS. 3-10), and allelic variants.

As used herein, “expression” refers to the process by whichpolynucleotides are transcribed into mRNA and/or translated intopeptides, polypeptides, or proteins. If the polynucleotide is derivedfrom genomic DNA, expression may include splicing of the mRNAtranscribed from the genomic DNA.

As used herein, “under transcriptional control” or “operably linked”refers to expression (e.g., transcription or translation) of apolynucleotide sequence which is controlled by an appropriatejuxtaposition of an expression control element and a coding sequence. Inone aspect, a DNA sequence is “operatively linked” to an expressioncontrol sequence when the expression control sequence controls andregulates the transcription of that DNA sequence.

As used herein, “coding sequence” is a sequence which is transcribed andtranslated into a polypeptide when placed under the control ofappropriate expression control sequences. The boundaries of a codingsequence are determined by a start codon at the 5′ (amino) terminus anda translation stop codon at the 3′ (carboxyl) terminus. A codingsequence can include, but is not limited to, a prokaryotic sequence,cDNA from eukaryotic mRNA, a genomic DNA sequence from eukaryotic (e.g.,mammalian) DNA, and even synthetic DNA sequences. A polyadenylationsignal and transcription termination sequence will usually be located 3′to the coding sequence.

As used herein, two coding sequences “correspond” to each other if thesequences or their complementary sequences encode the same amino acidsequences.

As used herein, “signal sequence” denotes the endoplasmic reticulumtranslocation sequence. This sequence encodes a signal peptide thatcommunicates to a cell to direct a polypeptide to which it is linked(e.g., via a chemical bond) to an endoplasmic reticulum vesicularcompartment, to enter an exocytic/endocytic organelle, to be deliveredeither to a cellular vesicular compartment, the cell surface or tosecrete the polypeptide. This signal sequence is sometimes clipped offby the cell in the maturation of a protein. Signal sequences can befound associated with a variety of proteins native to prokaryotes andeukaryotes.

As used herein, “trafficking” denotes movement or progression of thepolypeptide encoded by the improved LAMP Construct through cellularorganelles or compartments in the pathway from the rough endoplasmicreticulum to the endosomal/lysosomal compartment or related organelleswhere antigen processing and binding to MHC II occurs.

As used herein, an “improved LAMP Construct” and an “improved LAMPConstruct comprising an antigen” and an “improved LAMP Constructcomprising an antigen of interest” are used interchangeably. Thedifferent arrangements of the improved LAMP Constructs are illustratedin FIG. 1 as ILC1-ILC6. Moreover, the use of an “improved LAMPConstruct” encompasses both the polynucleotide sequence of the improvedLAMP Construct as well as the protein encoded by the polynucleotidesequence of the improved LAMP Construct.

As used herein, an “improved LAMP Construct delivery vehicle” is definedas any molecule or group of molecules or macromolecules that can carryan improved LAMP Construct into a host cell (e.g., such as genes or genefragments, antisense molecules, ribozymes, aptamers, and the like) andwhich occurs in association with an improved LAMP Construct as describedherein.

As used herein, “improved LAMP Construct delivery,” or “improved LAMPConstruct transfer,” refers to the introduction of the improved LAMPConstruct into a host cell, irrespective of the method used for theintroduction. The introduced improved LAMP Constructs may be stably ortransiently maintained in the host cell. Stable maintenance typicallyrequires that the introduced improved LAMP Construct either contains anorigin of replication compatible with the host cell or integrates into areplicon of the host cell such as an extrachromosomal replicon (e.g., aplasmid) or a nuclear or mitochondrial chromosome.

As used herein, a “viral improved LAMP Construct” refers to a virus orviral particle that comprises the improved LAMP Construct to bedelivered into a host cell, either in vivo, ex vivo or in vitro.Examples of viral improved LAMP Constructs include, but are not limitedto, adenovirus vectors, adeno-associated virus vectors, retroviralvectors, and the like. In aspects where gene transfer is mediated by anadenoviral vector, an improved LAMP Construct includes the adenovirusgenome or part thereof, and a selected, non-adenoviral gene, inassociation with adenoviral capsid proteins.

As used herein, “adenoviral-mediated gene transfer” or “adenoviraltransduction” refers to the process by which an improved LAMP Constructis transferred into a host cell by virtue of the adenovirus entering thecell. Preferably, the improved LAMP Construct is able to replicateand/or integrate and be transcribed within the cell.

As used herein, “adenovirus particles” are individual adenovirus virionscomprised of an external capsid and an improved LAMP Construct, wherethe capsid is further comprised of adenovirus envelope proteins. Theadenovirus envelope proteins may be modified to comprise a fusionpolypeptide which contains a polypeptide ligand covalently attached tothe viral protein, e.g., for targeting the adenoviral particle to aparticular cell and/or tissue type.

As used herein, the term “administering” or “immunizing” or “injecting”an improved LAMP Construct refers to transducing, transfecting,microinjecting, electroporating, or shooting the cell with the improvedLAMP Construct. In some aspects, improved LAMP Constructs are introducedinto a target cell by contacting the target cell with a delivery cell(e.g., by cell fusion or by lysing the delivery cell when it is inproximity to the target cell).

As used herein, the phrase “prime boost” describes the use of animproved LAMP Construct described herein used to prime a T-cell responsefollowed by the use of a second improved LAMP Construct comprising anantigen, a DNA vaccine comprising an antigen or a recombinant antigen toboost the response. These heterologous prime-boost immunizations elicitimmune responses of greater height and breadth than can be achieved bypriming and boosting with the same vector. The priming with an improvedLAMP Construct comprising an antigen initiates memory cells; the booststep expands the memory response. Preferably, use of the two differentagents do not raise responses against each other and thus do notinterfere with each other's activity. Mixtures of antigens arespecifically contemplated in the prime and/or boost step. Boosting canoccur one or multiple times.

As used herein, “hybridization” refers to a reaction in which one ormore polynucleotides react to form a complex that is stabilized viahydrogen bonding between the bases of the nucleotide residues. Thehydrogen bonding may occur by Watson-Crick base pairing, Hoogsteinbinding, or in any other sequence-specific manner. The complex maycomprise two strands forming a duplex structure, three or more strandsforming a multi-stranded complex, a single self-hybridizing strand, orany combination of these. A hybridization reaction may constitute a stepin a more extensive process, such as the initiation of a PCR reaction,or the enzymatic cleavage of a polynucleotide by a ribozyme.

As used herein, a polynucleotide or polynucleotide region (or apolypeptide or polypeptide region) which has a certain percentage (forexample, at least about 50%, at least about 60%, at least about 70%, atleast about 80%, at least about 85%, at least about 90%, at least about95%, at least about 99%) of “sequence identity” to another sequencemeans that, when maximally aligned, using software programs routine inthe art, that percentage of bases (or amino acids) are the same incomparing the two sequences.

Two sequences are “substantially homologous” or “substantially similar”when at least about 50%, at least about 60%, at least about 70%, atleast about 75%, and preferably at least about 80%, and most preferablyat least about 90 or 95% of the nucleotides match over the definedlength of the DNA sequences. Similarly, two polypeptide sequences are“substantially homologous” or “substantially similar” when at leastabout 50%, at least about 60%, at least about 66%, at least about 70%,at least about 75%, and preferably at least about 80%, and mostpreferably at least about 90 or 95% of the amino acid residues of thepolypeptide match over a defined length of the polypeptide sequence.Sequences that are substantially homologous can be identified bycomparing the sequences using standard software available in sequencedata banks. Substantially homologous nucleic acid sequences also can beidentified in a Southern hybridization experiment under, for example,stringent conditions as defined for that particular system. Definingappropriate hybridization conditions is within the skill of the art. Forexample, stringent conditions can be: hybridization at 5×SSC and 50%formamide at 42° C., and washing at 0.1×SSC and 0.1% sodium dodecylsulfate at 60° C. Further examples of stringent hybridization conditionsinclude: incubation temperatures of about 25 degrees C. to about 37degrees C.; hybridization buffer concentrations of about 6×SSC to about10×SSC; formamide concentrations of about 0% to about 25%; and washsolutions of about 6×SSC. Examples of moderate hybridization conditionsinclude: incubation temperatures of about 40 degrees C. to about 50degrees C.; buffer concentrations of about 9×SSC to about 2×SSC;formamide concentrations of about 30% to about 50%; and wash solutionsof about 5×SSC to about 2×SSC. Examples of high stringency conditionsinclude: incubation temperatures of about 55 degrees C. to about 68degrees C.; buffer concentrations of about 1×SSC to about 0.1×SSC;formamide concentrations of about 55% to about 75%; and wash solutionsof about 1×SSC, 0.1×SSC, or deionized water. In general, hybridizationincubation times are from 5 minutes to 24 hours, with 1, 2, or morewashing steps, and wash incubation times are about 1, 2, or 15 minutes.SSC is 0.15 M NaCl and 15 mM citrate buffer. It is understood thatequivalents of SSC using other buffer systems can be employed.Similarity can be verified by sequencing, but preferably, is also oralternatively, verified by function (e.g., ability to traffic to anendosomal compartment, and the like), using assays suitable for theparticular domain in question.

The terms “percent (%) sequence similarity”, “percent (%) sequenceidentity”, and the like, generally refer to the degree of identity orcorrespondence between different nucleotide sequences of nucleic acidmolecules or amino acid sequences of polypeptides that may or may notshare a common evolutionary origin (see Reeck et al., supra). Sequenceidentity can be determined using any of a number of publicly availablesequence comparison algorithms, such as BLAST, FASTA, DNA Strider, GCG(Genetics Computer Group, Program Manual for the GCG Package, Version 7,Madison, Wis.), etc.

To determine the percent identity between two amino acid sequences ortwo nucleic acid molecules, the sequences are aligned for optimalcomparison purposes. The percent identity between the two sequences is afunction of the number of identical positions shared by the sequences(i.e., percent identity=number of identical positions/total number ofpositions (e.g., overlapping positions)×100). In one embodiment, the twosequences are, or are about, of the same length. The percent identitybetween two sequences can be determined using techniques similar tothose described below, with or without allowing gaps. In calculatingpercent sequence identity, typically exact matches are counted.

The determination of percent identity between two sequences can beaccomplished using a mathematical algorithm. A non-limiting example of amathematical algorithm utilized for the comparison of two sequences isthe algorithm of Karlin and Altschul, Proc. Natl. Acad. Sci. USA 1990,87:2264, modified as in Karlin and Altschul, Proc. Natl. Acad. Sci. USA1993, 90:5873-5877. Such an algorithm is incorporated into the NBLASTand XBLAST programs of Altschul et al, J. Mol. Biol. 1990; 215: 403.BLAST nucleotide searches can be performed with the NBLAST program,score=100, wordlength=12, to obtain nucleotide sequences homologous tosequences of the invention. BLAST protein searches can be performed withthe XBLAST program, score=50, wordlength=3, to obtain amino acidsequences homologous to protein sequences of the invention. To obtaingapped alignments for comparison purposes, Gapped BLAST can be utilizedas described in Altschul et al, Nucleic Acids Res. 1997, 25:3389.Alternatively, PSI-Blast can be used to perform an iterated search thatdetects distant relationship between molecules. See Altschul et al.(1997) supra. When utilizing BLAST, Gapped BLAST, and PSI-Blastprograms, the default parameters of the respective programs (e.g.,XBLAST and NBLAST) can be used. See ncbi.nlm.nih.gov/BLAST/ on theWorldWideWeb.

Another non-limiting example of a mathematical algorithm utilized forthe comparison of sequences is the algorithm of Myers and Miller, CABIOS1988; 4: 11-17. Such an algorithm is incorporated into the ALIGN program(version 2.0), which is part of the GCG sequence alignment softwarepackage. When utilizing the ALIGN program for comparing amino acidsequences, a PAM120 weight residue table, a gap length penalty of 12,and a gap penalty of 4 can be used.

In a preferred embodiment, the percent identity between two amino acidsequences is determined using the algorithm of Needleman and Wunsch (J.Mol. Biol. 1970, 48:444-453), which has been incorporated into the GAPprogram in the GCG software package (Accelrys, Burlington, Mass.;available at accelrys.com on the WorldWideWeb), using either a Blossum62 matrix or a PAM250 matrix, a gap weight of 16, 14, 12, 10, 8, 6, or4, and a length weight of 1, 2, 3, 4, 5, or 6. In yet another preferredembodiment, the percent identity between two nucleotide sequences isdetermined using the GAP program in the GCG software package using aNWSgapdna.CMP matrix, a gap weight of 40, 50, 60, 70, or 80, and alength weight of 1, 2, 3, 4, 5, or 6. A particularly preferred set ofparameters (and the one that can be used if the practitioner isuncertain about what parameters should be applied to determine if amolecule is a sequence identity or homology limitation of the invention)is using a Blossum 62 scoring matrix with a gap open penalty of 12, agap extend penalty of 4, and a frameshift gap penalty of 5.

Another non-limiting example of how percent identity can be determinedis by using software programs such as those described in CurrentProtocols In Molecular Biology (F. M. Ausubel et al., eds., 1987)Supplement 30, section 7.7.18, Table 7.7.1. Preferably, defaultparameters are used for alignment. A preferred alignment program isBLAST, using default parameters. In particular, preferred programs areBLASTN and BLASTP, using the following default parameters: Geneticcode=standard; filter=none; strand=both; cutoff=60; expect=10;Matrix=BLOSUM62; Descriptions=50 sequences; sort by=HIGH SCORE;Databases=non-redundant, GenBank+EMBL+DDBJ+PDB+GenBank CDStranslations+SwissProtein+SPupdate+PIR. Details of these programs can befound at the following Internet address:http://www.ncbi.nlm.nih.gov/cgi-bin/BLAST.

Statistical analysis of the properties described herein may be carriedout by standard tests, for example, t-tests, ANOVA, or Chi squaredtests. Typically, statistical significance will be measured to a levelof p=0.05 (5%), more preferably p=0.01, p=0.001, p=0.0001, p=0.000001

“Conservatively modified variants” of domain sequences also can beprovided. With respect to particular nucleic acid sequences,conservatively modified variants refer to those nucleic acids whichencode identical or essentially identical amino acid sequences, or wherethe nucleic acid does not encode an amino acid sequence, to essentiallyidentical sequences. Specifically, degenerate codon substitutions can beachieved by generating sequences in which the third position of one ormore selected (or all) codons is substituted with mixed-base and/ordeoxyinosine residues (Batzer, et al., 1991, Nucleic Acid Res. 19: 5081;Ohtsuka, et al., 1985, J. Biol. Chem. 260: 2605-2608; Rossolini et al.,1994, Mol. Cell. Probes 8: 91-98).

The term “biologically active fragment”, “biologically active form”,“biologically active equivalent” of and “functional derivative” of awild-type protein, possesses a biological activity that is at leastsubstantially equal (e.g., not significantly different from) thebiological activity of the wild type protein as measured using an assaysuitable for detecting the activity.

As used herein, “in vivo” nucleic acid delivery, nucleic acid transfer,nucleic acid therapy” and the like, refer to the introduction of animproved LAMP Construct directly into the body of an organism, such as ahuman or non-human mammal, whereby the improved LAMP Construct isintroduced to a cell of such organism in vivo.

As used herein, the term “in situ” refers to a type of in vivo nucleicacid delivery in which the improved LAMP Construct is brought intoproximity with a target cell (e.g., the nucleic acid is not administeredsystemically). For example, in situ delivery methods include, but arenot limited to, injecting an improved LAMP Construct directly at a site(e.g., into a tissue, such as a tumor or heart muscle), contacting theimproved LAMP Construct with cell(s) or tissue through an open surgicalfield, or delivering the improved LAMP Constructs to a site using amedical access device such as a catheter.

As used herein, the term “isolated” or “purified” means separated (orsubstantially free) from constituents, cellular and otherwise, in whichthe polynucleotide, peptide, polypeptide, protein, antibody, orfragments thereof, are normally associated with in nature. For example,with respect to an improved LAMP Construct, an isolated polynucleotideis one that is separated from the 5′ and 3′ sequences with which it isnormally associated in the chromosome. As is apparent to those of skillin the art, a non-naturally occurring polynucleotide, peptide,polypeptide, protein, antibody, or fragments thereof, does not require“isolation” to distinguish it from its naturally occurring counterpart.By substantially free or substantially purified, it is meant at least50% of the population, preferably at least 70%, more preferably at least80%, and even more preferably at least 90%, are free of the componentswith which they are associated in nature.

As used herein, a “target cell” or “recipient cell” refers to anindividual cell or cell which is desired to be, or has been, a recipientof the improved LAMP Constructs described herein. The term is alsointended to include progeny of a single cell, and the progeny may notnecessarily be completely identical (in morphology or in genomic ortotal DNA complement) to the original parent cell due to natural,accidental, or deliberate mutation. A target cell may be in contact withother cells (e.g., as in a tissue) or may be found circulating withinthe body of an organism.

As used herein, a “subject” is a vertebrate, preferably a mammal, morepreferably a human. Mammals include, but are not limited to, murines,simians, humans, farm animals, sport animals, and pets. In otherpreferred embodiments, the “subject” is a rodent (e.g. a rat, a mouse, arabbit, a llama, camels, a cow, a guinea pig, a hamster, a dog, a cat, ahorse, a non-human primate, a simian (e.g. a monkey or ape), a monkey(e.g. marmoset, baboon, rhesus macaque), or an ape (e.g. gorilla,chimpanzee, orangutan, gibbon). In other embodiments, non-human mammals,especially mammals that are conventionally used as models fordemonstrating therapeutic efficacy in humans (e.g. murine, primate,porcine, canine, or rabbit animals) may be employed.

The terms “cancer,” “neoplasm,” and “tumor,” are used interchangeablyand in either the singular or plural form, refer to cells that haveundergone a malignant transformation that makes them pathological to thehost organism. Primary cancer cells transformation that makes thempathological to the host organism. Primary cancer cells (that is, cellsobtained from near the site of malignant transformation) can be readilydistinguished from non-cancerous cells by well-established techniques,particularly histological examination. The definition of a cancer cell,as used herein, includes not only a primary cancer cell, but any cellderived from a cancer cell ancestor. This includes metastasized cancercells, and in vitro cultures and cell lines derived from cancer cells.When referring to a type of cancer that normally manifests as a solidtumor, a “clinically detectable” tumor is one that is detectable on thebasis of tumor mass, e.g., by procedures such as CAT scan, MR imaging,X-ray, ultrasound or palpation, and/or which is detectable because ofthe expression of one or more cancer-specific antigens in a sampleobtainable from a patient.

In preferred embodiments, the cancer (including all stages ofprogression, including hyperplasia) is an adenocarcinoma, sarcoma, skincancer, melanoma, bladder cancer, brain cancer, breast cancer, uterinecancer, ovarian cancer, prostate cancer, lung cancer (including, but notlimited to NSCLC, SCLC, squamous cell cancer), colorectal cancer, analcancer, rectal cancer, cervical cancer, liver cancer, head and neckcancer, oral cancer, salivary gland cancer, esophageal cancer, pancreascancer, pancreatic ductal adenocarcinoma (PDA), renal cancer, stomachcancer, kidney cancer, multiple myeloma or cerebral cancer.

The improved LAMP Constructs described herein can also be used to treatallergies, such as for example, food allergies (e.g., peanut allergens,such as Ara H1, H2 and/or H3), or environmental allergens, such as forexample pollen (tree pollen, such as for example CRY J1 or CRY J2), dogdander, cat saliva, or dust mites. Other diseases and/or disordersinclude, for example, infectious disease and diabetes.

As used herein, the term “pharmaceutically acceptable carrier”encompasses any of the standard pharmaceutical carriers, such as aphosphate buffered saline solution, water, and emulsions, such as anoil/water or water/oil emulsion, and various types of wetting agents.Compositions comprising the improved LAMP Constructs also can includestabilizers and preservatives. For examples of carriers, stabilizers andadjuvants, see Martin Remington's Pharm. Sci., 15th Ed. (Mack Publ. Co.,Easton (1975)).

A cell has been “transformed”, “transduced”, or “transfected” by theimproved LAMP Constructs when such nucleic acids have been introducedinside the cell. Transforming DNA may or may not be integrated(covalently linked) with chromosomal DNA making up the genome of thecell. In prokaryotes, yeast, and mammalian cells for example, theimproved LAMP Constructs may be maintained on an episomal element, suchas a plasmid. In a eukaryotic cell, a stably transformed cell is one inwhich the improved LAMP Constructs have become integrated into achromosome so that it is inherited by daughter cells through chromosomereplication. This stability is demonstrated by the ability of theeukaryotic cell to establish cell lines or clones comprised of apopulation of daughter cells containing the improved LAMP Constructs. A“clone” is a population of cells derived from a single cell or commonancestor by mitosis. A “cell line” is a clone of a primary cell that iscapable of stable growth in vitro for many generations (e.g., at leastabout 10).

As used herein, an “effective amount” is an amount sufficient to affectbeneficial or desired results, e.g., such as an effective amount of theimproved LAMP Construct transfer and/or expression, and/or theattainment of a desired therapeutic endpoint. An effective amount can beadministered in one or more administrations, applications or dosages. Inone aspect, an effective amount of an improved LAMP Construct is anamount sufficient to transform/transduce/transfect at least one cell ina population of cells comprising at least two cells.

As used herein, a “therapeutically effective amount” is used herein tomean an amount sufficient to prevent, correct and/or normalize anabnormal physiological response. In one aspect, a “therapeuticallyeffective amount” is an amount sufficient to reduce by at least about 30percent, more preferably by at least 50 percent, most preferably by atleast 90 percent, a clinically significant feature of pathology, such asfor example, allergic response, size of a tumor mass, antibodyproduction, cytokine production, fever or white cell count, etc.

An “antibody” is any immunoglobulin, including antibodies and fragmentsthereof, that binds a specific antigen. The term encompasses polyclonal,monoclonal, and chimeric antibodies (e.g., bispecific antibodies). An“antibody combining site” is that structural portion of an antibodymolecule comprised of heavy and light chain variable and hypervariableregions that specifically binds antigen. Exemplary antibody moleculesare intact immunoglobulin molecules, substantially intact immunoglobulinmolecules, and those portions of an immunoglobulin molecule thatcontains the paratope, including Fab, Fab′, F(ab′)₂ and F(v) portions,which portions are preferred for use in the therapeutic methodsdescribed herein. Thus, the term antibody encompasses not only wholeantibody molecules, but also antibody fragments as well as variants(including derivatives such as fusion proteins) of antibodies andantibody fragments. Examples of molecules which are described by theterm “antibody” in this application include, but are not limited to:single chain Fvs (scFvs), Fab fragments, Fab′ fragments, F(ab′)₂,disulfide linked Fvs (sdFvs), Fvs, and fragments comprising oralternatively consisting of, either a VL or a VH domain. The term“single chain Fv” or “scFv” as used herein refers to a polypeptidecomprising a VL domain of an antibody linked to a VH domain of anantibody. See Carter (2006) Nature Rev. Immunol. 6:243.

Additionally, antibodies of the invention include, but are not limitedto, monoclonal, multi-specific, bi-specific, human, humanized, mouse, orchimeric antibodies, single chain antibodies, camelid antibodies, Fabfragments, F(ab′) fragments, anti-idiotypic (anti-Id) antibodies(including, e.g., anti-Id antibodies to antibodies of the invention),domain antibodies and epitope-binding fragments of any of the above. Theimmunoglobulin molecules of the invention can be of any type (e.g., IgG,IgE, IgM, IgD, IgA and IgY), class (e.g., IgG1, IgG2, IgG3, IgG4, IgA1and IgA2) or subclass of immunoglobulin molecule.

Most preferably, the antibodies are human antibodies. As used herein,“human” antibodies include antibodies having the amino acid sequence ofa human immunoglobulin and include antibodies isolated from humanimmunoglobulin libraries and xenomice or other organisms that have beengenetically engineered to produce human antibodies. The improved LAMPConstructs described herein can be used in combination with knowntechniques for generating human antibodies and human monoclonalantibodies as described in the exemplified protocols, see, e.g., PCTpublications WO 98/24893; WO 92/01047; WO 96/34096; WO 96/33735;European Patent No. 0 598 877; U.S. Pat. Nos. 5,413,923; 5,625,126;5,633,425; 5,569,825; 5,661,016; 5,545,806; 5,814,318; 5,885,793;5,916,771; and 5,939,598; and Lonberg and Huszar, Int. Rev. Immunol.13:65-93 (1995).

Human antibodies or “humanized” chimeric monoclonal antibodies can beproduced using the improved LAMP Constructs in combination withtechniques described herein or otherwise known in the art. For example,standard methods for producing chimeric antibodies are known in the art.See, for review the following references: Morrison, Science 229:1202(1985); Oi et al., BioTechniques 4:214 (1986); Cabilly et al., U.S. Pat.No. 4,816,567; Taniguchi et al., EP 171496; Morrison et al., EP 173494;Neuberger et al., WO 8601533; Robinson et al., WO 8702671; Boulianne etal., Nature 312:643 (1984); Neuberger et al., Nature 314:268 (1985).

The antibodies of the present invention may be monovalent, bivalent,trivalent or multivalent. For example, monovalent scFvs can bemultimerized either chemically or by association with another protein orsubstance. A scFv that is fused to a hexahistidine tag or a Flag tag canbe multimerized using Ni-NTA agarose (Qiagen) or using anti-Flagantibodies (Stratagene, Inc.). Additionally, the improved LAMPConstructs can be used to generate monospecific, bispecific, trispecificor of greater multispecificity for the encoded antigen(s) contained inthe improved LAMP Construct. See, e.g., PCT publications WO 93/17715; WO92/08802; WO 91/00360; WO 92/05793; Tutt, et al., J. Immunol. 147:60-69(1991); U.S. Pat. Nos. 4,474,893; 4,714,681; 4,925,648; 5,573,920;5,601,819; Kostelny et. al., J. Immunol. 148:1547-1553 (1992).

An “epitope” is a structure, usually made up of a short peptide sequenceor oligosaccharide, that is specifically recognized or specificallybound by a component of the immune system. T-cell epitopes havegenerally been shown to be linear oligopeptides. Two epitopes correspondto each other if they can be specifically bound by the same antibody.Two epitopes correspond to each other if both are capable of binding tothe same B cell receptor or to the same T cell receptor, and binding ofone antibody to its epitope substantially prevents binding by the otherepitope (e.g., less than about 30%, preferably, less than about 20%, andmore preferably, less than about 10%, 5%, 1%, or about 0.1% of the otherepitope binds). In the present invention, multiple epitopes can make upan antigen.

The term “antigen” or “antigen of interest” as used herein covers anypolypeptide sequence encoded by a polynucleotide sequence cloned intothe improved LAMP Construct which is used to elicit an innate oradaptive immune response. An “antigen” encompasses both a single antigenas well as multiple antigenic sequences (derived from the same ordifferent proteins) cloned into the improved LAMP Construct.

The term “antigen presenting cell” as used herein includes any cellwhich presents on its surface an antigen in association with a majorhistocompatibility complex molecule, or portion thereof, or,alternatively, one or more non-classical MHC molecules, or a portionthereof. Examples of suitable APCs are discussed in detail below andinclude, but are not limited to, whole cells such as macrophages,dendritic cells, B cells, hybrid APCs, and foster antigen presentingcells.

As used herein an “engineered antigen-presenting cell” refers to anantigen-presenting cell that has a non-natural molecular moiety on itssurface. For example, such a cell may not naturally have a costimulatoron its surface or may have an additional artificial costimulator inaddition to a natural costimulator on its surface, or may express anon-natural class II molecule on its surface. In preferred embodiments,the engineered antigen-presenting cell has the antigen expressed fromthe improved LAMP Construct on its surface.

As used herein, “immune effector cells” refers to cells capable ofbinding an antigen and which mediate an immune response. These cellsinclude, but are not limited to, T cells, B cells, monocytes,macrophages, NK cells and cytotoxic T lymphocytes (CTLs), for exampleCTL lines, CTL clones, and CTLs from tumor, inflammatory, or otherinfiltrates.

As used herein, “partially human” refers to a nucleic acid havingsequences from both a human and a non-human vertebrate. In the contextof partially human sequences, the partially human nucleic acids havesequences of human immunoglobulin coding regions and sequences based onthe non-coding sequences of the endogenous immunoglobulin region of thenon-human vertebrate. The term “based on” when used with reference toendogenous non-coding sequences from a non-human vertebrate refers tosequences that correspond to the non-coding sequence and share arelatively high degree of homology with the non-coding sequences of theendogenous loci of the host vertebrate, e.g., the non-human vertebratefrom which the ES cell is derived. Preferably, the non-coding sequencesshare at least an 80%, more preferably 90% homology with thecorresponding non-coding sequences found in the endogenous loci of thenon-human vertebrate host cell into which a partially human moleculecomprising the non-coding sequences has been introduced.

The term “immunoglobulin variable region” as used herein refers to anucleotide sequence that encodes all or a portion of a variable regionof an antibody molecule or all or a portion of a regulatory nucleotidesequence that controls expression of an antibody molecule.Immunoglobulin regions for heavy chains may include but are not limitedto all or a portion of the V, D, J, and switch regions, includingintrons. Immunoglobulin region for light chains may include but are notlimited to the V and J regions, their upstream flanking sequences,introns, associated with or adjacent to the light chain constant regiongene.

By “transgenic animal” is meant a non-human animal, usually a mammal,having an exogenous nucleic acid sequence present as an extrachromosomalelement in a portion of its cells or stably integrated into its germline DNA (i.e., in the genomic sequence of most or all of its cells). Ingenerating a transgenic animal comprising human sequences, a partiallyhuman nucleic acid is introduced into the germ line of such transgenicanimals by genetic manipulation of, for example, embryos or embryonicstem cells of the host animal according to methods well known in theart.

A “vector” includes plasmids and viruses and any DNA or RNA molecule,whether self-replicating or not, which can be used to transform ortransfect a cell.

As used herein, a “genetic modification” refers to any addition,deletion or disruption to a cell's normal nucleotides. Art recognizedmethods include viral mediated gene transfer, liposome mediatedtransfer, transformation, transfection and transduction, e.g.,viral-mediated gene transfer such as the use of the improved LAMPConstructs based on DNA viruses such as adenovirus, adeno-associatedvirus and herpes virus, as well as retroviral based vectors.

The practice of the present invention employs, unless otherwiseindicated, conventional molecular biology, microbiology, and recombinantDNA techniques within the skill of the art. Such techniques areexplained fully in the literature. See, e.g., Maniatis, Fritsch &Sambrook, In Molecular Cloning: A Laboratory Manual (1982); DNA Cloning:A Practical Approach, Volumes I and II (D. N. Glover, ed., 1985);Oligonucleotide Synthesis (M. J. Gait, ed., 1984); Nucleic AcidHybridization (B. D. Hames & S. J. Higgins, eds., 1985); Transcriptionand Translation (B. D. Hames & S. I. Higgins, eds., 1984); Animal CellCulture (R. I. Freshney, ed., 1986); Immobilized Cells and Enzymes (IRLPress, 1986); B. Perbal, A Practical Guide to Molecular Cloning (1984).

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. All publications mentionedherein are incorporated by reference for the purpose of describing anddisclosing devices, formulations and methodologies that may be used inconnection with the presently described invention

LAMP Constructs

LAMP-1, as deduced from a cDNA clone (Chen, et al., J. Biol. Chem. 263:8754, 1988) consists of a polypeptide core of about 382 amino acids witha large (346-residue) lumenal amino-terminal domain followed by a24-residue hydrophobic transmembrane region and short (12-residue)carboxyl-terminal cytoplasmic tail. See, FIGS. 2A and 2B. The lumenaldomain is highly glycosylated, being substituted with about 20asparagine linked complex-type oligosaccharides and consists of twoapproximately 160-residue “homology domains” that are separated by aproline/serine-rich hinge region. Each of these “homology domains”contains 4 uniformly spaced cysteine residues, disulfide bonded to formfour 36-38-residue loops symmetrically placed within the two halves ofthe lumenal domain (Arterburn, et al., J. Biol. Chem. 265: 7419, 1990;see, also Chen, et al., J. Biol. Chem. 25: 263(18): 8754-8, 1988). FIG.2A schematically shows the conserved domains between LAMP-1, LAMP-2,LAMP-3, Endolyn, LIMBIC, LAMPS, or Macrosailin.

Previously reported LAMP constructs comprise the following elements inthis specific arrangement:

(a) a full lumenal domain of LAMP-1 protein, the antigen and then thefull transmembrane/cytoplasmic tail of LAMP-1 protein; or

(b) the antigen and the full transmembrane/cytoplasmic tail of a LAMP-1protein. In example (a), the antigenic sequence is inserted in betweenthe full lumenal domain of a LAMP-1 protein and the LAMP-1 fulltransmembrane domain/cytoplasmic tail. Both constructs have been shownto successfully target an antigenic sequence to the lysosome/endosomeand will be referred to as “complete LAMP Constructs” as shown in FIG. 1as compared to the improved LAMP Constructs ILC1-ILC6 described herein.The improved LAMP Constructs described herein do not include thecomplete LAMP Constructs described in the prior art.

Although it has been widely reported in the literature that fragmentssmaller than the full lumenal domain of LAMP-1 were not effective ingenerating a robust immune response (see, e.g. Godinho et al.) theinventors unexpectedly discovered that specific fragments, in certainarrangements, did in fact effectively present antigens to the immunesystem, generating a robust immune response, including the generation ofa different repitoire of antibodies. For example, the inventors haveidentified that the minimal LAMP lumenal domain fragment that iseffective for generating a robust immune response is not the fulllumenal domain (as widely reported in the literature) but rather asingle Homology Domain of the Lumenal Domain of a LAMP Protein.

For example, constructs can comprise, not the full lumenal domain, butinstead a single Homology Domain of the Lumenal Domain of a LAMPProtein. As used herein, the “Homology Domain” comprises at least the 4uniformly spaced cysteine residues shown in FIGS. 3-10. These cysteineresides are labeled 1, 2, 3, and 4 (and in LIMP-2 and Macrosailin—fivecysteines are identified, LIMBIC—six cysteines are identified andEndolyn—eight cysteines are identified) in each Homology Domain as shownin FIGS. 3-10 and are defined herein as the “Cysteine ConservedFragment.” Additional amino acids can be included to either theN-terminus end and/or the C-terminus end of the Cysteine ConservedFragment to generate, up to and including a full Homology Domain of aLAMP protein. These additional added amino acids can be derived from theHomology Domain from which the Cysteine Conserved Fragment is derived orfrom other LAMP Protein Homology Domains. Thus, as used herein, a LAMPHomology Domain comprises and/or consists of one Cysteine ConservedFragment. At least two LAMP Homology Domains make up the Lumenal Domainof LAMP-1, LAMP-2, LAMP-3, or Endolyn.

Specifically, in one preferred embodiment, the improved LAMP Constructcomprises at least one antigen of interest fused to the N-terminus ofthe lumenal domain of a LAMP protein, at least one homology domain of aLAMP protein, or at least one Cysteine Conserved Fragment of a LAMPprotein. See, for example ILC-2 and ILC-6 of FIG. 1. In preferredembodiments, these constructs also comprise a transmembrane domain of aLAMP protein, and/or the cytosolic tail of a LAMP protein. In otherpreferred embodiments, when an antigen contains a transmembrane domain,the transmembrane domain of a LAMP protein and/or the cytosolic tail ofa LAMP protein is unnecessary. In preferred embodiments, two homologydomains are included in the improved LAMP Construct (e.g., ILC-1 of FIG.1). In further preferred embodiments, the two homology domains arederived from a LAMP-1, LAMP-2, LAMP-3, or an Endolyn protein.Alternatively, the two homology domains are derived from different LAMPproteins. In these constructs comprising two homology domains, a LAMPhinge domain may also be included. The improved LAMP Constructsdescribed in this paragraph are unexpected in view of the prior art asthe antigen has always been placed in between the full lumenal LAMP-1domain and the full LAMP-1 transmembrane/cytoplasmic tail, as fragmentsof the lumenal domain have not been reported to be effective ingenerating a robust immune response.

In another preferred embodiment, the improved LAMP Construct comprisesat least one antigen of interest fused to the C-terminus of a singlehomology domain of a LAMP protein or a single Cysteine ConservedFragment of a LAMP protein. See, for example, ILC-3 and ILC-5 of FIG. 1.In preferred embodiments, these constructs also comprise a transmembranedomain of a LAMP protein, and/or the cytosolic tail of a LAMP protein.In other preferred embodiments, when an antigen contains a transmembranedomain, the transmembrane domain of a LAMP protein and/or the cytosolictail of a LAMP protein is unnecessary. The improved LAMP Constructsdescribed in this paragraph are unexpected in view of the prior art asdescribed above.

In another preferred embodiment, the improved LAMP Construct comprisesat least one antigen of interest fused in between a first homologydomain of a LAMP protein and a second homology domain of a LAMP protein(or at least between two Cysteine Conserved Fragments). See, forexample, ILC-4 of FIG. 1. In preferred embodiments, these constructsalso comprise a transmembrane domain of a LAMP protein, and/or thecytosolic tail of a LAMP protein. In preferred embodiments, the twohomology domains are derived from LAMP-1, LAMP-2, LAMP-3, or an Endolynprotein. In these constructs, the antigen may be placed in the LAMPhinge region. Alternatively, two homology domains from two differentLAMP proteins may be used. This arrangement of at least one antigen ofinterest fused in between two LAMP homology domains (including CysteineConserved Fragments) is unexpected in view of the prior art as describedabove.

Each of the improved LAMP Constructs defined above can be generatedusing the domains defined in the Figures. For example, it isspecifically contemplated that the domains included in the improved LAMPConstruct illustrated in FIG. 1, for example, can originate fromsequences derived from orthologous sequences. See, FIGS. 3-10 forexample. It is expressly contemplated that the equivalent domainsdefined in FIGS. 2A and 2B be used to generate the improved LAMPConstructs illustrated in FIG. 1 for orthologous sequences. Moreover,the orthologous sequences shown in FIGS. 3-10 are representative of thesequences that can be used to generate the domains. It is well withinthe skill in the art to identify other orthologous sequences and/orisotypes and comparing them to the alignments shown in FIGS. 3-10. Thus,by identifying the equivalent boundaries defined in FIGS. 2A and 2B fora human LAMP protein with the alignments shown in FIGS. 3-10, one cangenerate the improved LAMP Constructs illustrated in FIG. 1.

As would be well understood by the skilled artisan, the boundaries ofeach domain are an approximation and may be adjusted at least 1, 2, 3,4, 5, 6, 7, 8, 9, or 10 amino acids based on cloning considerations andrestriction enzyme placement. Therefore, when a particular domain (e.g.,a LAMP Homology Domain) is included in the improved LAMP Construct, theamino acids beginning and ending of the domain may be adjust by at least1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acids as those boundaries definedin FIG. 2B.

Each of the improved LAMP Constructs described above can additionallycomprise a signal sequence and/or additional amino acids in between eachdomain for cloning purposes as is well known in the art. Additionally,the LAMP homologous domains, the LAMP lumenal domain, the LAMPtransmembrane domain, and/or the LAMP cytosolic tail domain canoriginate from the same LAMP protein (e.g., human LAMP-1) or differentLAMP proteins (e.g., lumenal domain from human LAMP-1 and transmembranedomain from human LAMP-2, and/or mixing of orthologous domains in thesame gene family (e.g., LAMP-1) or different gene family (LAMP-1 andLAMP-2).

Polypeptide variants of the described LAMP Constructs are contemplated.For example, polypeptides at least about 60%, at least about 70%, atleast about 75%, at least about 80%, at least about 85%, at least about90%, at least about 95%, 96%, 97%, 98% or 99% identity to any of theimproved LAMP Constructs described herein as well as polynucleotidesencoding these variants. Variants of the improved LAMP Constructs retainthe ability to function by targeting the antigenic sequence to thelysosome. For example, a modified lumenal sequence must retain theability to traffic both membrane and non-membrane antigenic materials toan endosomal compartment with at least about 50%, at least about 60%, atleast 70%, at least about 80%, at least about 90%, or at least about100% efficacy compared to the original domain sequence, i.e., anefficacy that results in sufficient antigen presentation by a cellcomprising the chimeric sequence for it to mount an immune response. Inone aspect, sequences containing a suitable trafficking signal may beidentified by constructing an improved LAMP Construct containing thewell-characterized antigenic domain of ovalbumin, a transmembranedomain, and the cytoplasmic domain of a protein containing a putativelysosomal/endosomal targeting signal. Efficiency of targeting can bemeasured by determining the ability of antigen presenting cells,expressing the improved LAMP Construct, to stimulate HAepitope-specific, MHC class II restricted T-cells (see, e.g., Example 5of U.S. Pat. No. 5,633,234).

Polynucleotides encoding any of the described improved LAMP Constructsare preferred embodiments of the invention, along with polynucleotidesat least about 60%, at least about 70%, at least about 75%, at leastabout 80%, at least about 85%, at least about 90%, at least about 95%,96%, 97%, 98% or 99% identity to any of the improved LAMP Constructpolynucleotides described herein. Variants of the improved LAMPConstructs retain the ability to function by targeting the antigenicsequence to the lysosome. For example, a modified lumenal sequence mustretain the ability to traffic both membrane and non-membrane antigenicmaterials to an endosomal compartment with at least about 50%, at leastabout 60%, at least 70%, at least about 80%, at least about 90%, or atleast about 100% efficacy compared to the original domain sequence,i.e., an efficacy that results in sufficient antigen presentation by acell comprising the chimeric sequence for it to mount an immuneresponse. In one aspect, sequences containing a suitable traffickingsignal may be identified by constructing an improved LAMP Constructcontaining the well-characterized antigenic domain of ovalbumin, atransmembrane domain, and the cytoplasmic domain of a protein containinga putative lysosomal/endosomal targeting signal. Efficiency of targetingcan be measured by determining the ability of antigen presenting cells,expressing the improved LAMP Construct, to stimulate HAepitope-specific, MHC class II restricted T-cells (see, e.g., Example 5of U.S. Pat. No. 5,633,234).

Assembly of Sequences Encoding Improved LAMP Constructs

Procedures for constructing improved LAMP Constructs comprising theantigen of interest are well known in the art (see e.g., Williams, etal., J. Cell Biol. 111: 955, 1990). DNA sequences encoding the desiredsegments can be obtained from readily available recombinant DNAmaterials such as those available from the American Type CultureCollection, 12301 Parklawn Drive, Rockville, Md. 20852, U.S.A., or fromDNA libraries that contain the desired DNA.

For example, the DNA segments corresponding to the desired domainsequences can be assembled with appropriate control and signal sequencesusing routine procedures of recombinant DNA methodology. See, e.g., asdescribed in U.S. Pat. No. 4,593,002, and Langford, et al., Molec. Cell.Biol. 6: 3191, 1986.

A DNA sequence encoding a protein or polypeptide can be synthesizedchemically or isolated by one of several approaches. The DNA sequence tobe synthesized can be designed with the appropriate codons for thedesired amino acid sequence. In general, one will select preferredcodons for the intended host in which the sequence will be used forexpression. The complete sequence may be assembled from overlappingoligonucleotides prepared by standard methods and assembled into acomplete coding sequence. See, e.g., Edge, Nature 292: 756, 1981;Nambair, et al. Science 223: 1299, 1984; Jay, et al., J. Biol. Chem.259: 6311, 1984.

In one aspect, one or more of the nucleic acids encoding the domainsequences of the improved LAMP Construct are isolated individually usingthe polymerase chain reaction (M. A. Innis, et al., In PCR Protocols: AGuide to Methods and Applications, Academic Press, 1990). The domainsare preferably isolated from publicly available clones known to containthem, but they may also be isolated from genomic DNA or cDNA libraries.Preferably, isolated fragments are bordered by compatible restrictionendonuclease sites which allow an improved LAMP Construct encoding theantigen sequence to be constructed. This technique is well known tothose of skill in the art. Domain sequences may be fused directly toeach other (e.g., with no intervening sequences), or inserted into oneanother (e.g., where domain sequences are discontinuous), or may beseparated by intervening sequences (e.g., such as linker sequences).

The basic strategies for preparing oligonucleotide primers, probes andDNA libraries, as well as their screening by nucleic acid hybridization,are well known to those of ordinary skill in the art. See, e.g.,Sambrook, et al., 1989, supra; Perbal, 1984, supra. The construction ofan appropriate genomic DNA or cDNA library is within the skill of theart. See, e.g., Perbal, 1984, supra. Alternatively, suitable DNAlibraries or publicly available clones are available from suppliers ofbiological research materials, such as Clonetech and Stratagene, as wellas from public depositories such as the American Type CultureCollection.

Selection may be accomplished by expressing sequences from an expressionlibrary of DNA and detecting the expressed peptides immunologically.Clones which express peptides that bind to MHC II molecules and to thedesired antibodies/T cell receptors are selected. These selectionprocedures are well known to those of ordinary skill in the art (see,e.g., Sambrook, et al., 1989, supra).

Once a clone containing the coding sequence for the desired polypeptidesequence has been prepared or isolated, the sequence can be cloned intoany suitable vector, preferably comprising an origin of replication formaintaining the sequence in a host cell.

Nucleic Acid Delivery Vehicles

In one aspect, a vaccine composition comprising an improved LAMPConstruct is introduced into a cell. The cell may be a host cell forreplicating the nucleic acid or for expressing the improved LAMPConstruct. Preferably, the host cell for expressing the improved LAMPConstruct is an antigen presenting cell (described further below).

In preferred embodiments, the improved LAMP Construct further comprisesa polynucleotide sequence for insertion into a target cell and anexpression control sequence operably linked thereto to controlexpression of the polynucleotide sequence (e.g., transcription and/ortranslation) in the cell. Examples include plasmids, phages,autonomously replicating sequences (ARS), centromeres, and othersequences which are able to replicate or be replicated in vitro or in ahost cell (e.g., such as a bacterial, yeast, or insect cell) and/ortarget cell (e.g., such as a mammalian cell, preferably an antigenpresenting cell) and/or to convey the sequences encoding the improvedLAMP Construct to a desired location within the target cell.

Recombinant expression vectors may be derived from micro-organisms whichreadily infect animals, including man, horses, cows, pigs, llamas,giraffes, dogs, cats or chickens. Preferred vectors include those whichhave already been used as live vaccines, such as vaccinia. Theserecombinants can be directly inoculated into a host, conferring immunitynot only to the microbial vector, but also to express foreign antigens.Preferred vectors contemplated herein as live recombinant vaccinesinclude RNA viruses, adenovirus, herpesviruses, poliovirus, and vacciniaand other pox viruses, as taught in Flexner, Adv. Pharmacol. 21: 51,1990, for example.

Expression control sequences include, but are not limited to, promotersequences to bind RNA polymerase, enhancer sequences or negativeregulatory elements to bind to transcriptional activators andrepressors, respectively, and/or translation initiation sequences forribosome binding. For example, a bacterial expression vector can includea promoter such as the lac promoter and for transcription initiation,the Shine-Dalgarno sequence and the start codon AUG (Sambrook, et al.,1989, supra). Similarly, a eukaryotic expression vector preferablyincludes a heterologous, homologous, or chimeric promoter for RNApolymerase II, a downstream polyadenylation signal, the start codon AUG,and a termination codon for detachment of a ribosome.

Expression control sequences may be obtained from naturally occurringgenes or may be designed. Designed expression control sequences include,but are not limited to, mutated and/or chimeric expression controlsequences or synthetic or cloned consensus sequences. Vectors thatcontain both a promoter and a cloning site into which a polynucleotidecan be operatively linked are well known in the art. Such vectors arecapable of transcribing RNA in vitro or in vivo, and are commerciallyavailable from sources such as Stratagene (La Jolla, Calif.) and PromegaBiotech (Madison, Wis.).

In order to optimize expression and/or transcription, it may benecessary to remove, add or alter 5′ and/or 3′ untranslated portions ofthe vectors to eliminate extra, or alternative translation initiationcodons or other sequences that may interfere with, or reduce,expression, either at the level of transcription or translation.Alternatively, consensus ribosome binding sites can be insertedimmediately 5′ of the start codon to enhance expression. A wide varietyof expression control sequences—sequences that control the expression ofa DNA sequence operatively linked to it—may be used in these vectors toexpress the DNA sequences of this invention. Such useful expressioncontrol sequences include, for example, the early or late promoters ofSV40, CMV, vaccinia, polyoma, adenovirus, herpes virus and othersequences known to control the expression of genes of mammalian cells,and various combinations thereof.

In one aspect, the improved LAMP Construct comprises an origin ofreplication for replicating the vector. Preferably, the origin functionsin at least one type of host cell which can be used to generatesufficient numbers of copies of the sequence for use in delivery to atarget cell. Suitable origins therefore include, but are not limited to,those which function in bacterial cells (e.g., such as Escherichia sp.,Salmonella sp., Proteus sp., Clostridium sp., Klebsiella sp., Bacillussp., Streptomyces sp., and Pseudomonas sp.), yeast (e.g., such asSaccharamyces sp. or Pichia sp.), insect cells, and mammalian cells. Inone preferred aspect, an origin of replication is provided whichfunctions in the target cell into which the nucleic acid deliveryvehicle is introduced (e.g., a mammalian cell, such as a human cell). Inanother aspect, at least two origins of replication are provided, onethat functions in a host cell and one that functions in a target cell.

The improved LAMP Construct may alternatively, or additionally, comprisesequences to facilitate integration of at least a portion of the nucleicacid deliver vector into a target cell chromosome. For example, theimproved LAMP Construct may comprise regions of homology to target cellchromosomal DNA. In one aspect, the delivery vector comprises two ormore recombination sites which flank a nucleic acid sequence encodingthe improved LAMP Construct.

The vector may additionally comprise a detectable and/or selectablemarker to verify that the vector has been successfully introduced in atarget cell and/or can be expressed by the target cell. These markerscan encode an activity, such as, but not limited to, production of RNA,peptide, or protein, or can provide a binding site for RNA, peptides,proteins, inorganic and organic compounds or compositions and the like.

Examples of detectable/selectable markers genes include, but are notlimited to: DNA segments that encode products which provide resistanceagainst otherwise toxic compounds (e.g., antibiotics); DNA segments thatencode products which are otherwise lacking in the recipient cell (e.g.,tRNA genes, auxotrophic markers); DNA segments that encode productswhich suppress the activity of a gene product; DNA segments that encodeproducts which can be readily identified (e.g., phenotypic markers suchas beta-galactosidase, a fluorescent protein (GFP, CFP, YFG, BFP, RFP,EGFP, EYFP, EBFP, dsRed, mutated, modified, or enhanced forms thereof,and the like), and cell surface proteins); DNA segments that bindproducts which are otherwise detrimental to cell survival and/orfunction; DNA segments that otherwise inhibit the activity of othernucleic acid segments (e.g., antisense oligonucleotides); DNA segmentsthat bind products that modify a substrate (e.g., restrictionendonucleases); DNA segments that can be used to isolate or identify adesired molecule (e.g., segments encoding specific protein bindingsites); primer sequences; DNA segments, which when absent, directly orindirectly confer resistance or sensitivity to particular compounds;and/or DNA segments that encode products which are toxic in recipientcells.

The marker gene can be used as a marker for conformation of successfulgene transfer and/or to isolate cells expressing transferred genesand/or to recover transferred genes from a cell. For example, in oneaspect, the marker gene is used to isolate and purify antigen presentingcells expressing the improved LAMP Constructs.

Substantially similar genes may be provided, e.g., genes with greaterthan about 50%, greater than about 70%, greater than 80%, greater thanabout 90%, and preferably, greater than about 95% identity to a knowngene. Substantially similar domain sequences may initially be identifiedby selecting a sequence which specifically hybridizes to a domainsequence of interest under stringent hybridization conditions.Performing assays to determine the suitability of homologous, variant,or modified domain sequences is merely a matter of screening forsequences which express the appropriate activity. Such screening isroutine in the art.

The improved LAMP Construct may be provided as naked nucleic acids or ina delivery vehicle associated with one or more molecules forfacilitating entry of a nucleic acid into a cell. Suitable deliveryvehicles include, but are not limited to: liposomal formulations,polypeptides, polysaccharides, lipopolysaccharides, viral formulations(e.g., including viruses, viral particles, artificial viral envelopesand the like), cell delivery vehicles, and the like.

Lipid-Based Formulations

Delivery vehicles designed to facilitate intracellular delivery of theimproved LAMP Constructs must interact with both non-polar and polarenvironments (in or on, for example, the plasma membrane, tissue fluids,compartments within the cell, and the like). Therefore, preferably,delivery vehicles are designed to contain both polar and non-polardomains or a translocating sequence for translocating an improved LAMPConstruct into a cell.

Compounds having polar and non-polar domains are termed amphiphiles.Cationic amphiphiles have polar groups that are capable of beingpositively charged at, or around, physiological pH for interacting withnegatively charged polynucleotides such as DNA.

The improved LAMP Constructs described herein can be provided informulations comprising lipid monolayers or bilayers to facilitatetransfer of the vectors across a cell membrane. Liposomes or any form oflipid membrane, such as planar lipid membranes or the cell membrane ofan intact cell, e.g., a red blood cell, can be used. Liposomalformulations can be administered by any means, including administrationintravenously or orally.

Liposomes and liposomal formulations can be prepared according tostandard methods and are well known in the art, see, e.g., Remington's;Akimaru, 1995, Cytokines Mol. Ther. 1: 197-210; Alving, 1995, Immunol.Rev. 145: 5-31; Szoka, 1980, Ann. Rev. Biophys. Bioeng. 9: 467; U.S.Pat. Nos. 4,235,871; 4,501,728; and 4,837,028. In one aspect, theliposome comprises a targeting molecule for targeting aliposome:improved LAMP Construct complex to a particular cell type. In aparticularly preferred aspect, a targeting molecule comprises a bindingpartner (e.g., a ligand or receptor) for a biomolecule (e.g., a receptoror ligand) on the surface of a blood vessel or a cell found in a targettissue.

Liposome charge is an important determinant in liposome clearance fromthe blood, with negatively charged liposomes being taken up more rapidlyby the reticuloendothelial system (Juliano, 1975, Biochem. Biophys. Res.Commun. 63: 651) and thus having shorter half-lives in the bloodstream.Incorporating phosphatidylethanolamine derivatives enhances thecirculation time by preventing liposomal aggregation. For example,incorporation of N-(omega-carboxy)acylamidophosphatidylethanolaminesinto large unilamellar vesicles of L-alpha-distearoylphosphatidylcholinedramatically increases the in vivo liposomal circulation lifetime (see,e.g., Ahl, 1997, Biochim. Biophys. Acta 1329: 370-382). Liposomes withprolonged circulation half-lives are typically desirable for therapeuticand diagnostic uses. For a general discussion of pharmacokinetics, see,e.g., Remington's, Chapters 37-39, Lee, et al., In PharmacokineticAnalysis: A Practical Approach (Technomic Publishing AG, Basel,Switzerland 1996).

Typically, liposomes are prepared with about 5 to 15 mole percentnegatively charged phospholipids, such as phosphatidylglycerol,phosphatidylserine or phosphatidyl-inositol. Added negatively chargedphospholipids, such as phosphatidylglycerol, also serve to preventspontaneous liposome aggregation, and thus minimize the risk ofundersized liposomal aggregate formation. Membrane-rigidifying agents,such as sphingomyelin or a saturated neutral phospholipid, at aconcentration of at least about 50 mole percent, and 5 to 15 molepercent of monosialylganglioside can also impart desirably liposomeproperties, such as rigidity (see, e.g., U.S. Pat. No. 4,837,028).

Additionally, the liposome suspension can include lipid-protectiveagents which protect lipids against free-radical and lipid-peroxidativedamages on storage. Lipophilic free-radical quenchers, such asalpha-tocopherol and water-soluble iron-specific chelators, such asferrioxianine, are preferred.

The improved LAMP Constructs of the invention can include multilamellarvesicles of heterogeneous sizes. For example, vesicle-forming lipids canbe dissolved in a suitable organic solvent or solvent system and driedunder vacuum or an inert gas to form a thin lipid film. If desired, thefilm can be redissolved in a suitable solvent, such as tertiary butanol,and then lyophilized to form a more homogeneous lipid mixture which isin a more easily hydrated powderlike form. This film is covered with anaqueous solution of the peptide or polypeptide complex and allowed tohydrate, typically over a 15 to 60 minute period with agitation. Thesize distribution of the resulting multilamellar vesicles can be shiftedtoward smaller sizes by hydrating the lipids under more vigorousagitation conditions or by adding solubilizing detergents such asdeoxycholate. The hydration medium preferably comprises the nucleic acidat a concentration which is desired in the interior volume of theliposomes in the final liposome suspension.

Following liposome preparation, the liposomes can be sized to achieve adesired size range and relatively narrow distribution of liposome sizes.One preferred size range is about 0.2 to 0.4 microns, which allows theliposome suspension to be sterilized by filtration through aconventional filter, typically a 0.22 micron filter. Filtersterilization can be carried out on a high throughput basis if theliposomes have been sized down to about 0.2 to 0.4 microns. Severaltechniques are available for sizing liposome to a desired size (see,e.g., U.S. Pat. No. 4,737,323).

Suitable lipids include, but are not limited to, DOTMA (Felgner, et al.,1987, Proc. Natl. Acad. Sci. USA 84: 7413-7417), DOGS or Transfectain™(Behr, et al., 1989, Proc. Natl. Acad. Sci. USA 86: 6982-6986), DNERIEor DORIE (Felgner, et al., Methods 5: 67-75), DC-CHOL (Gao and Huang,1991, BBRC 179: 280-285), DOTAP™ (McLachlan, et al., 1995, Gene Therapy2: 674-622), Lipofectamine™. and glycerolipid compounds (see, e.g.,EP901463 and WO98/37916).

Other molecules suitable for complexing with the improved LAMPConstructs include cationic molecules, such as, polyamidoamine (Haenslerand Szoka, 1993, Bioconjugate Chem. 4: 372-379), dendritic polysine (WO95/24221), polyethylene irinine or polypropylene h-nine (WO 96/02655),polylysine (U.S. Pat. No. 5,595,897; FR 2 719 316), chitosan (U.S. Pat.No. 5,744,166), DNA-gelatin coacervates (see, e.g., U.S. Pat. Nos.6,207,195; 6,025,337; 5,972,707) or DEAE dextran (Lopata, et al., 1984,Nucleic Acid Res. 12: 5707-5717).

Viral-Based Gene Delivery Vehicles

In one aspect, the improved LAMP Construct delivery vehicle comprises avirus or viral particle. In this aspect, preferably, the improved LAMPConstruct comprises a viral vector. Viral vectors, such as retroviruses,adenoviruses, adeno-associated viruses and herpes viruses, are oftenmade up of two components, a modified viral genome and a coat structuresurrounding it (see, e.g., Smith et al., 1995, Ann. Rev. Microbiol. 49:807-838), although sometimes viral vectors are introduced in naked formor coated with proteins other than viral proteins. Most current vectorshave coat structures similar to a wild-type virus. This structurepackages and protects the viral nucleic acid and provides the means tobind and enter target cells.

Preferably, viral vectors comprising the improved LAMP Constructsdescribed herein are modified from wild-type viral genomes to disablethe growth of the virus in a target cell while enabling the virus togrow in a host cell (e.g., such as a packaging or helper cell) used toprepare infectious particles. Vector nucleic acids generally essentialcis-acting viral sequences for replication and packaging in a helperline and expression control sequences for regulating the expression of apolynucleotide being delivered to a target cell. Other viral functionsare expressed in trans in specific packaging or helper cell lines as areknown in the art.

Preferred improved LAMP Constructs are viral vectors derived from avirus selected from the group consisting of herpes viruses,cytomegaloviruses, foamy viruses, lentiviruses, Semliki forrest virus,AAV (adeno-associated virus), poxviruses, adenovirases and retroviruses.Such viral vectors are well known in the art.

In one preferred aspect, a viral vector used is an adenoviral vector.The adenoviral genome consists of a linear double-stranded DNA moleculeof approximately 36 kb carrying more than about thirty genes necessaryto complete the viral replication cycle. The early genes are dividedinto 4 regions (E1 to E4) that are essential for viral replication withthe exception of the E3 region, which is believed to modulate theanti-viral host immune response. The E1 region (EIA and EIB) encodesproteins responsible for the regulation of transcription of the viralgenome. Expression of the E2 region genes (E2A and E2B) leads to thesynthesis of the polypeptides needed for viral replication. The proteinsencoded by the E3 region prevent cytolysis by cytotoxic T cells andtumor necrosis factor (Wold and Gooding, 1991, Virology 184: 1-8). Theproteins encoded by the E4 region are involved in DNA replication, lategene expression and splicing and host cell shut off (Halbert, et al.,1985, J. Virol. 56: 250-257). The late genes generally encode structuralproteins contributing to the viral capsid. In addition, the adenoviralgenome carries at cis-acting 5′ and 3′ ITRs (Inverted Terminal Repeat)and packaging sequences essential for DNA replication. The ITRs harbororigins of DNA replication while the encapsidation region is requiredfor the packaging of adenoviral DNA into infectious particles.

Adenoviral vectors can be engineered to be conditionally replicative(CRAd vectors) in order to replicate selectively in specific cells(e.g., such as proliferative cells) as described in Heise and Kim (2000,J. Clin. Invest. 105: 847-851). In another aspect, an adenoviral vectoris replication-defective for the E1 function (e.g., by total or partialdeletion or mutagenesis of E1). The adenoviral backbone of the vectormay comprise additional modifications (deletions, insertions ormutations in one or more viral genes). An example of an E2 modificationis illustrated by the thermosensitive mutation localized on the DBP (DNABinding Protein) encoding gene (Ensinger et al., 1972, J. Virol. 10:328-339). The adenoviral sequence may also be deleted of all or part ofthe E4 region (see, e.g., EP 974 668; Christ, et al., 2000, Human GeneTher. 11: 415-427; Lusky, et al., 1999, J. Virol. 73: 8308-8319).Additional deletions within the non-essential E3 region may allow thesize of the polynucleotide being delivered to be increased (Yeh, et al.,1997, FASEB Journal 11: 615 623). However, it may be advantageous toretain all or part of the E3 sequences coding for polypeptides (e.g.,such as gp19k) allowing the virus to escape the immune system (Gooding,et al., 1990, Critical Review of Immunology 10: 53-71) or inflammatoryreactions (EP 00440267.3).

Second generation vectors retaining the ITRs and packaging sequences andcomprising substantial genetic modifications to abolish the residualsynthesis of the viral antigens also may be used in order to improvelong-term expression of the expressed gene in the transduced cells (see,e.g., WO 94/28152; Lusky, et al., 1998, J. Virol 72: 2022-2032).

The improved LAMP Constructs being introduced into the cell may beinserted in any location of the viral genome, with the exception of thecis-acting sequences. Preferably, it is inserted in replacement of adeleted region (E1, E3 and/or E4), preferably, within a deleted E1region.

Adenoviruses can be derived from any human or animal source, inparticular canine (e.g. CAV-1 or CAV-2 Genbank ref. CAVIGENOM andCAV77082, respectively), avian (Genbank ref. AAVEDSDNA), bovine (such asBAV3; Reddy, et al., 1998, J. Virol. 72: 1394 1402), murine (Genbankref. ADRMUSMAVI), ovine, feline, porcine or simian sources oralternatively, may be a hybrid virus. Any serotype can be employed.However, the human adenoviruses of the C sub-group are preferred,especially adenoviruses 2 (Ad2) and 5 (Ad5). Such viruses are available,for example, from the ATCC.

Adenoviral particles or empty adenoviral capsids also can be used totransfer improved LAMP Constructs by a virus-mediated cointernalizationprocess as described in U.S. Pat. No. 5,928,944. This process can beaccomplished in the presence of cationic agent(s) such as polycarbenesor lipid vesicles comprising one or more lipid layers.

Adenoviral particles may be prepared and propagated according to anyconventional technique in the field of the art (e.g., WO 96/17070) usinga complementation cell line or a helper virus, which supplies in transthe missing viral genes necessary for viral replication. The cell lines293 (Graham et al., 1977, J. Gen. Virol. 36: 59-72) and PERC6 (Fallauxet al., 1998, Human Gene Therapy 9: 1909-1917) are commonly used tocomplement E1 deletions. Other cell lines have been engineered tocomplement defective vectors (Yeh, et al., 1996, J. Virol. 70: 559-565;Kroughak and Graham, 1995, Human Gene Ther. 6: 1575-1586; Wang, et al.,1995, Gene Ther. 2: 775-783; Lusky, et al., 1998, J. Virol. 72:2022-203; EP 919627 and WO 97/04119). The adenoviral particles can berecovered from the culture supernatant but also from the cells afterlysis and optionally further purified according to standard techniques(e.g., chromatography, ultracentrifugation, as described in WO 96/27677,WO 98/00524 WO 98/26048 and WO 00/50573).

Cell-type specific targeting may be achieved with vectors derived fromadenoviruses having a broad host range by the modification of viralsurface proteins. For example, the specificity of infection ofadenoviruses is determined by the attachment to cellular receptorspresent at the surface of permissive cells. In this regard, the fiberand penton present at the surface of the adenoviral capsid play acritical role in cellular attachment (Defer, et al., 1990, J. Virol. 64:3661-3673). Thus, cell targeting of adenoviruses can be carried out bygenetic modification of the viral gene encoding fiber and/or penton, togenerate modified fiber and/or penton capable of specific interactionwith unique cell surface receptors. Examples of such modifications aredescribed in Wickarn, et al., 1997, J. Virol. 71: 8221-8229; Arriberg,et al., 1997, Virol. Chem 268: 6866-6869; Roux, et al., 1989, Proc.Natl. Acad. Sci. USA 86: 9079-9083; Miller and Vile, 1995, FASEB J. 9:190-199; WO 93/09221, and in WO 95/28494.

In a particularly preferred aspect, adeno-associated viral sequences areused as vectors. Vectors derived from the human parvovirus AAV-2(adeno-associated virus type 2) are among the most promising genedelivery vehicles currently being developed. Several of the features ofthis system for packaging a single-stranded DNA suggest it as a possiblealternative to naked DNA for delivery. A primary attractive feature, incontrast to other viral vectors such as vaccinia or adenovirus, is thatAAV vectors do not express any viral genes. The only viral DNA sequencesincluded in the vaccine construct are the 145 bp inverted terminalrepeats (ITR). Thus, as in immunization with naked DNA, the only geneexpressed is that of the antigen, or antigen chimera. Additionally, AAVvectors are known to transduce both dividing and non-dividing cells,such as human peripheral blood monocyte-derived dendritic cells, withpersistent transgene expression, and with the possibility of oral andintranasal delivery for generation of mucosal immunity. Moreover, theamount of DNA required appears to be much less by several orders ofmagnitude, with maximum responses at doses of 10¹⁰ to 10¹¹ particles orcopies of DNA in contrast to naked DNA doses of 50 ug or about 10¹⁵copies.

In one aspect, AAV vectors are packaged by co-transfection of a suitablecell line (e.g., human 293 cells) with the DNA contained in the AAV ITRchimeric protein encoding constructs and an AAV helper plasmid ACG2containing the AAV coding region (AAV rep and cap genes) without theITRs. The cells are subsequently infected with the adenovirus Ad5.Vectors can be purified from cell lysates using methods known in the art(e.g., such as cesium chloride density gradient ultracentrifugation) andare validated to ensure that they are free of detectablereplication-competent AAV or adenovirus (e.g., by a cytopathic effectbioassay). AAV titer may be determined by quantitative PCR with virusDNA samples prepared after digestion with proteinase K. Preferably,vector titers produced by such a method are approximately 5×10¹² to1×10¹³ DNase resistant particles per ml.

In other aspects, retroviral vectors are used. Retroviruses are a classof integrative viruses which replicate using a virus-encoded reversetranscriptase, to replicate the viral RNA genome into double strandedDNA which is integrated into chromosomal DNA of the infected cells(e.g., target cells). Such vectors include those derived from murineleukemia viruses, especially Moloney (Gilboa, et al., 1988, Adv. Exp.Med. Biol. 241: 29) or Friend's FB29 strains (WO 95/01447). Generally, aretroviral vector is deleted of all or part of the viral genes gag, poland env and retains 5′ and 3′ LTRs and an encapsidation sequence. Theseelements may be modified to increase expression level or stability ofthe retroviral vector. Such modifications include the replacement of theretroviral encapsidation sequence by one of a retrotransposon such asVL30 (see, e.g., U.S. Pat. No. 5,747,323). Preferably, the improved LAMPConstruct is inserted downstream of the encapsidation sequence,preferably in opposite direction relative to the retroviral genome. Cellspecific targeting may be achieved by the conjugation of antibodies orantibody fragments to the retroviral envelope protein as is known in theart.

Retroviral particles are prepared in the presence of a helper virus orin an appropriate complementation (packaging) cell line which containsintegrated into its genome the retroviral genes for which the retroviralvector is defective (e.g. gag/pol and env). Such cell lines aredescribed in the prior art (Miller and Rosman, 1989, BioTechniques 7:980; Danos and Mulligan, 1988, Proc. Natl. Acad. Sci. USA 85: 6460;Markowitz, et al., 1988, Virol. 167: 400). The product of the env geneis responsible for the binding of the viral particle to the viralreceptors present on the surface of the target cell and, thereforedetermines the host range of the retroviral particle. in the context ofthe invention, it is advantageous to use a packaging cell line, such asthe PA317 cells (ATCC CRL 9078) or 293EI6 (WO97/35996) containing anamphotropic envelope protein, to allow infection of human and otherspecies' target cells. The retroviral particles are preferably recoveredfrom the culture supernatant and may optionally be further purifiedaccording to standard techniques (e.g. chromatography,ultracentrifugation).

Other suitable viruses include poxviruses. The genome of several membersof poxyiridae has been mapped and sequenced. A poxyiral vector may beobtained from any member of the poxyiridae, in particular canarypox,fowlpox and vaccinia virus. Suitable vaccinia viruses include, but arenot limited to, the Copenhagen strain (Goebel, et al., 1990, Virol. 179:247-266; Johnson, et al., 1993, Virol. 196: 381-401), the Wyeth strainand the modified Ankara (MVA) strain (Antoine, et al., 1998, Virol. 244:365-396). The general conditions for constructing a vaccinia virusvector are known in the art (see, e.g., EP 83 286 and EP 206 920; Mayret al., 1975, Infection 3: 6-14; Sutter and Moss, 1992, Proc. Natl.Acad. Sci. USA 89: 10847-10851). Preferably, the polynucleotide ofinterest is inserted within a non-essential locus such as the noncodingintergenic regions or any gene for which inactivation or deletion doesnot significantly impair viral growth and replication.

Poxyiral particles are prepared as described in the art (Piccini, etal., 1987, Methods of Enzymology 153: 545-563; U.S. Pat. Nos. 4,769,330;4,772,848; 4,603,112; 5,100,587 and 5,179,993). Generally, a donorplasmid is constructed, amplified by growth in E. coli and isolated byconventional procedures. Then, it is introduced into a suitable cellculture (e.g. chicken embryo fibroblasts) together with a poxvirusgenome, to produce, by homologous recombination, poxyiral particles.These can be recovered from the culture supernatant or from the culturedcells after a lysis step (e.g., chemical lysis, freezing/thawing,osmotic shock, sonication and the like). Consecutive rounds of plaquepurification can be used to remove contaminating wild type virus. Viralparticles can then be purified using the techniques known in the art(e.g., chromatographic methods or ultracentrifugation on cesium chlorideor sucrose gradients).

The use of vaccinia as a live virus vaccine in the global campaign toeradicate smallpox made vaccinia an obvious choice for development as alive recombinant vaccine vector. Live recombinant vaccinia virusesexpressing close to 100 different foreign proteins have been reported,and a number of these are effective experimental vaccines (reviewed byMoss and Flexner, 1987). Vaccinia is particularly versatile as anexpression vector because of its large genomic size, capability ofaccepting at least 25,000 base pairs of foreign DNA, and its ability toinfect most eukaryotic cell types, including insect cells (ibid.).Unlike other DNA viruses, poxviruses replicate exclusively in thecytoplasm of infected cells, reducing the possibility of geneticexchange of recombinant viral DNA with the host chromosome. Recombinantvaccinia vectors have been shown to properly process and expressproteins from a variety of sources including man, other mammals,parasites, RNA and DNA viruses, bacteria and bacteriophage.

The expression of DNA encoding a foreign protein is controlled by hostvirus regulatory elements, including upstream promoter sequences and,where necessary, RNA processing signals. Insertion of foreign DNA intononessential regions of the vaccinia virus genome has been carried outby homologous recombination (Panicali, et al., Proc. Nat'l. Acad. Sci,USA, 79: 4927, 1982; Mackett, et al., Proc. Nat'l. Acad. Sci. USA, 79:7415, 1982).

Expression of antigens by the improved LAMP Construct may occur becauseof transcriptional regulatory elements at or near the site of insertionor by more precise genetic engineering. Plasmid vectors that greatlyfacilitate insertion and expression of foreign genes have beenconstructed (Mackett, et al., J. Virol, 49: 857, 1982). These vectorscontain an expression site, composed of a vaccinia transcriptionalpromoter and one or more unique restriction endonuclease sites forinsertion of the foreign coding sequence flanked by DNA from anonessential region of the vaccinia genome. The choice of promoterdetermines both the time (e.g., early or late) and level of expression,whereas the flanking DNA sequence determines the site of homologousrecombination.

Only about one in a thousand virus particles produced by this procedureis a recombinant. Although recombinant virus plaques can be identifiedby DNA hybridization, efficient selection procedures have beendeveloped. By using segments of nonessential vaccinia virus thymidinekinase (TK) gene as flanking sequences, the foreign gene recombines intothe TK locus and by insertion inactivates the TK gene. Selection of TKvirus is achieved by carrying out the virus plaque assay in TK cells inthe presents of 5-bromodeoxyuridine. Phosphorylation of the nucleosideanalogue and consequent lethal incorporation into viral DNA occurs onlyin cells infected with TK+ parental virus. Depending on the efficiencyof the transfection and recombination, up to 80 of the plaques aredesired recombinants, and the rest are spontaneous TK mutants.

Plasmid vectors that contain the E. coli beta-galactosidase gene, aswell as an expression site for a second gene, permit an alternativemethod of distinguishing recombinant from parental virus (Chakrabarti,et al., Mol. Cell. Biol., 5: 3403, 1985). Plaques formed by suchrecombinants can be positively identified by the blue color that formsupon addition of an appropriate indicator. By combining both TKselection and beta-galactosidase expression, recombinant virus isreadily and quickly isolated. The recombinants are then amplified bypropagation in suitable cell lines and expression of the inserted geneis checked by appropriate enzymological, immunological or physicalprocedures.

An upper limit to the amount of genetic information that can be added tothe vaccinia virus genome is not yet known. However, the addition ofnearly 25,000 base pairs of foreign DNA had no apparent deleteriouseffect on virus yield (Smith, et al., Gene, 25:21, 1983). Were itnecessary, large segments of the vaccinia virus genome could be deletedto provide additional capacity (Moss, et al., J. Virol. 40: 387, 1981).

Viral capsid molecules may include targeting moieties to facilitatetargeting and/or entry into cells. Suitable targeting molecules,include, but are not limited to: chemical conjugates, lipids,glycolipids, hormones, sugars, polymers (e.g. PEG, polylysine, PEI andthe like), peptides, polypeptides (see, e.g., WO 94/40958), vitamins,antigens, lectins, antibodies and fragments thereof. Preferably, suchtargeting molecules recognize and bind to cell-specific markers,tissue-specific markers, cellular receptors, viral antigens, antigenicepitopes or tumor-associated markers.

Compositions comprising an improved LAMP Construct based on viralparticles may be formulated in the form of doses of between 10 and 10¹⁴i.u. (infectious units), and preferably, between 10 and 10¹¹ i.u. Thetiter may be determined by conventional techniques. The doses of LAMPConstructs are preferably comprised between 0.01 and 10 mg/kg, moreespecially between 0.1 and 2 mg/kg.

Self-Replicating RNA

Self-replicating RNA virus vectors can also be constructed using theimproved LAMP Constructs as described herein. For example, alphaviruses,flaviviruses, measle virus and rhabdoviruses can be used to generateself-replicating RNA virus vaccines. Preferred strains ofself-replicating RNA viruses include, but are not limited to rabiesvirus (RABV), vesicular stomatisitis virus (VSV), West Nile virus,Kunjin virus, Semliki Forest virus (SFV), Sindbis virus (SIN) and/orVenezuelan equine encephalitis virus (VEE).

Self-replicating RNA viruses express the native antigen upon deliveryinto tissue, thus mimicking live attenuated vaccines without having therisk of reversion to pathogenicity. They also stimulate the innateimmune system, thus potentiating responses. See, e.g., Ljungberg, K.“Self-replicating alphavirus RNA vaccines,” Expert Rev Vaccines(2):177-94 (2015); Lundstrom, K., “Oncolytic Alphaviruses in CancerImmunotherapy”, Vaccines 5:9 (2017); Lundstrom, K. “Replicon RNA ViralVectors as Vaccines,” Vaccines 4:39 (2016) (hereby incorporated byreference in their entirety). Use of self-replicating vaccinescomprising the improved LAMP Constructs described herein can also beused in prime-boost protocols.

Moreover, self-replicating RNA viruses can also be encapsulated byliposomes, as described herein, to improve delivery and targeting.Immunization with self-replicating RNA viruses comprising the improvedLAMP Constructs described herein may provide higher transient expressionlevels of antigens resulting in generation of neutralizing antibodyresponses and protection against lethal challenges under safeconditions.

Cell-Based Delivery Vehicles

The improved LAMP Constructs according to the invention can be deliveredto target cells by means of other cells (“delivery cells) which comprisethe constructs. Methods for introducing constructs into cells are knownin the art and include microinjection of DNA into the nucleus of a cell(Capechi, et al., 1980, Cell 22: 479-488); transfection with CaPo₄ (Chenand Okayama, 1987, Mol. Cell Biol. 7: 2745 2752), electroporation (Chu,et al., 1987, Nucleic Acid Res. 15: 1311-1326); lipofection/liposomefusion (Feigner, et al., 1987, Proc. Natl. Acad. Sci. USA 84: 7413-7417)and particle bombardment (Yang, et al., 1990, Proc. Natl. Acad. Sci. USA87: 9568-9572). Suitable cells include autologous and non-autologouscells, and may include xenogenic cells. Delivery cells may be induced todeliver their contents to the target cells by inducing their death(e.g., by providing inducible suicide genes to these cells).

Accessory Molecules

The compositions comprising the improved LAMP Constructs according tothe invention may comprise one or more accessory molecules forfacilitating the introduction of an improved LAMP Construct into a celland/or for enhancing a particular therapeutic effect and/or enhancingantibody production.

In addition, the composition comprising the improved LAMP Constructaccording to the present invention may include one or more stabilizingsubstance(s), such as lipids, nuclease inhibitors, hydrogels,hyaluronidase (WO 98/53853), collagenase, polymers, chelating agents (EP890362), in order to inhibit degradation within the animal/human bodyand/or improve transfection/infection of the vector into a target cell.Such substances may be used alone or in combination (e.g., cationic andneutral lipids).

It has also been shown that adenovirus proteins are capable ofdestabilizing endosomes and enhancing the uptake of DNA into cells. Themixture of adenoviruses to solutions containing a lipid-complexed DNAvector or the binding of DNA to polylysine covalently attached toadenoviruses using protein cross-linking agents may substantiallyimprove the uptake and expression of an improved LAMP Construct (see,e.g., Curiel, et al., 1992, Am. I. Respir. Cell. Mol. Biol. 6: 247-252).

Host Cells

Improved LAMP Constructs according to the invention can be expressed ina variety of host cells, including, but not limited to: prokaryoticcells (e.g., E. coli, Staphylococcus sp., Bacillus sp.); yeast cells(e.g., Saccharomyces sp.); insect cells; nematode cells; plant cells;amphibian cells (e.g., Xenopus); avian cells; and mammalian cells (e.g.,human cells, mouse cells, mammalian cell lines, primary culturedmammalian cells, such as from dissected tissues).

The molecules can be expressed in host cells isolated from an organism,host cells which are part of an organism, or host cells which areintroduced into an organism. In one aspect, improved LAMP Constructs areexpressed in host cells in vitro, e.g., in culture. In another aspect,improved LAMP Constructs are expressed in a transgenic organism (e.g., atransgenic mouse, rat, rabbit, pig, primate, etc.) that comprisessomatic and/or germline cells comprising nucleic acids encoding theimproved LAMP Constructs. Methods for constructing transgenic animalsare well known in the art and are routine.

Improved LAMP Constructs also can be introduced into cells in vitro, andthe cells (e.g., such as stem cells, hematopoietic cells, lymphocytes,and the like) can be introduced into the host organism. The cells may beheterologous or autologous with respect to the host organism. Forexample, cells can be obtained from the host organism, improved LAMPConstructs introduced into the cells in vitro, and then reintroducedinto the host organism.

Antigen Presenting Cells

In a preferred aspect of the invention, an improved LAMP Construct asdescribed herein is introduced into a natural or engineered antigenpresenting cell.

The term “antigen presenting cell” (APC) as used herein intends any cellwhich presents on its surface an antigen in association with a majorhistocompatibility complex molecule, preferably a class II molecule, orportion thereof. Examples of suitable APCs are discussed in detail belowand include, but are not limited to, whole cells such as macrophages,dendritic cells, B cells, hybrid APCs, and foster antigen presentingcells. Methods of making hybrid APCs are described and known in the art.

Dendritic cells (DCs) are potent antigen-presenting cells. It has beenshown that DCs provide all the signals required for T cell activationand proliferation. These signals can be categorized into two types. Thefirst type, which gives specificity to the immune response, is mediatedthrough interaction between the T-cell receptor/CD3 (“TCR/CD3”) complexand an antigenic peptide presented by a major histocompatibility complex(“MHC” defined above) class I or II protein on the surface of APCs. Thisinteraction is necessary, but not sufficient, for T cell activation tooccur. In fact, without the second type of signals, the first type ofsignals can result in T cell anergy. The second type of signals, calledco-stimulatory signals, is neither antigen-specific nor MHC-restricted,and can lead to a full proliferation response of T cells and inductionof T cell effector functions in the presence of the first type ofsignals.

Several molecules have been shown to enhance co-stimulatory activity.These include, but are not limited to, heat stable antigen (HSA),chondroitin sulfate-modified MHC invariant chain (Ii-CS), intracellularadhesion molecule I (ICAM-1), and B7 co-stimulatory molecule on thesurface of APCs and its counter-receptor CD28 or CTLA-4 on T cells.

Other important co-stimulatory molecules are CD40, CD54, CD80, CD86. Asused herein, the term “co-stimulatory molecule” encompasses any singlemolecule or combination of molecules which, when acting together with apeptide/MHC complex bound by a TCR on the surface of a T cell, providesa co-stimulatory effect which achieves activation of the T cell thatbinds the peptide. The term thus encompasses B7, or other co-stimulatorymolecule(s) on an APC, fragments thereof (alone, complexed with anothermolecule(s), or as part of a fusion protein) which, together withpeptide/MHC complex, binds to a cognate ligand and result in activationof the T cell when the TCR on the surface of the T cell specificallybinds the peptide. Co-stimulatory molecules are commercially availablefrom a variety of sources, including, for example, Beckman Coulter.

In one aspect of the invention, the method described in Romani et al.,J. Immunol. Methods 196: 135-151, 1996, and Bender et al, J. Immunol.Methods 196: 121-135, 1996, are used to generate both immature andmature dendritic cells from the peripheral blood mononuclear cells(PBMCs) of a mammal, such as a murine, simian or human. Briefly,isolated PBMCs are pre-treated to deplete T- and B-cells by means of animmunomagnetic technique. Lymphocyte-depleted PBMC are then cultured forin RPMI medium 9 e.g., about 7 days), supplemented with human plasma(preferably autologous plasma) and GM-CSF/IL-4, to generate dendriticcells. Dendritic cells are non-adherent when compared to their monocyteprogenitors. Thus, on approximately day 7, non-adherent cells areharvested for further processing.

The dendritic cells derived from PBMC in the presence of GM-CSF and IL-4are immature, in that they can lost the nonadherence property and revertback to macrophage cell fate if the cytokine stimuli are removed fromthe culture. The dendritic cells in an immature state are very effectivein processing native protein antigens for the MHC class II restrictedpathway (Romani, et al., J. Exp. Med. 169:1169, 1989). Furthermaturation of cultured dendritic cells is accomplished by culturing for3 days in a macrophage-conditioned medium (CM), which contains thenecessary maturation factors. Mature dendritic cells are less able tocapture new proteins for presentation but are much better at stimulatingresting T cells (both CD4 and CD8) to grow and differentiate.

Mature dendritic cells can be identified by their change in morphology,such as the formation of more motile cytoplasmic processes; by theirnonadherence; by the presence of at least one of the following markers:CD83, CD68, HLA-DR or CD86; or by the loss of Fc receptors such as CD115 (reviewed in Steinman, Annu. Rev. Immunol. 9: 271, 1991). Maturedendritic cells can be collected and analyzed using typicalcytofluorography and cell sorting techniques and devices, such asFACScan and FACStar. Primary antibodies used for flow cytometry arethose specific to cell surface antigens of mature dendritic cells andare commercially available. Secondary antibodies can be biotinylated Igsfollowed by FITC- or PE-conjugated streptavidin.

Alternatively, others have reported that a method for upregulating(activating) dendritic cells and converting monocytes to an activateddendritic cell phenotype. This method involves the addition of calciumionophore to the culture media convert monocytes into activateddendritic cells. Adding the calcium 21 ionophore A23187, for example, atthe beginning of a 24-48 hour culture period resulted in uniformactivation and dendritic cell phenotypic conversion of the pooled“monocyte plus DC” fractions: characteristically, the activatedpopulation becomes uniformly CD 14 (Leu M3) negative, and upregulatesHLA-DR, HLA-DQ, ICAM-1,137.1, and 137.2. Furthermore, this activatedbulk population functions as well on a small numbers basis as a furtherpurified. Specific combination(s) of cytokines have been usedsuccessfully to amplify (or partially substitute) for theactivation/conversion achieved with calcium ionophore: these cytokinesinclude but are not limited to G-CSF, GM-CSF, IL-2, and IL-4. Eachcytokine when given alone is inadequate for optimal upregulation.

The second approach for isolating APCs is to collect the relativelylarge numbers of precommitted APCs already circulating in the blood.Previous techniques for isolating committed APCs from human peripheralblood have involved combinations of physical procedures such asmetrizamide gradients and adherence/nonadherence steps (Freudenthal etal. PNAS 87: 7698-7702, 1990); Percoll gradient separations(Mehta-Damani, et al., J. Immunol. 153: 996-1003, 1994); andfluorescence activated cell sorting techniques (Thomas et al., J.Immunol. 151: 6840-52, 1993).

There are many other methods routine in the art for isolatingprofessional antigen presenting cells (or their precursors) and thatsuch methods and others which may be developed are not limiting and areencompassed within the scope of the invention.

In one embodiment, the APCs and therefore the cells presenting one ormore antigens are autologous. In another embodiment, the APCs presentingthe antigen are allogeneic, i.e., derived from a different subject.

As discussed herein, improved LAMP Constructs can be introduced intoAPCs using the methods described above or others known in the art,including, but not limited to, transfection, electroporation, fusion,microinjection, viral-based delivery, or cell based delivery. Arthur etal., Cancer Gene Therapy 4(1): 17-25, 1997, reports a comparison of genetransfer methods in human dendritic cells.

Known, partial and putative human leukocyte antigen (HLA), the geneticdesignation for the human MHC, amino acid and nucleotide sequences,including the consensus sequence, are published (see, e.g., Zemmour andParham, Immunogenetics 33: 310-320, 1991), and cell lines expressing HLAvariants are known and generally available as well, many from theAmerican Type Culture Collection (“ATCC”). Therefore, using PCR, MHCclass II-encoding nucleotide sequences are readily operatively linked toan expression vector of this invention that is then used to transform anappropriate cell for expression therein.

Professional APCs can be used, such as macrophages, B cells, monocytes,dendritic cells, and Langerhans cells. These are collected from theblood or tissue of 1) an autologous donor; 2) a heterologous donorhaving a different HLA specificity then the host to be treated; or 3)from a xenogeneic donor of a different species using standard procedures(Coligan, et. al., Current Protocols in Immunology, sections 3 and 14,1994). The cells may be isolated from a normal host or a patient havingan infectious disease, cancer, autoimmune disease, or allergy.

Professional APCs may be obtained from the peripheral blood usingleukopheresis and “FICOLL/HYPAQUE” density gradient centrifugation(stepwise centrifugation through Ficoll and discontinuous Percolldensity gradients). Procedures are utilized which avoid the exposure ofthe APCs to antigens which could be internalized by the APCs, leading toactivation of T cells not specific for the antigens of interest.

Cells which are not naturally antigen presenting can be engineered to beantigen presenting by introducing sequences encoding appropriatemolecules. For example, nucleic acid sequences encoding MHC class IImolecules, accessory molecules, co-stimulatory molecules and antigenprocessing assisting molecules can be introduced after direct synthesis,cloning, purification of DNA from cells containing such genes, and thelike. One expedient means to obtain genes for encoding the moleculesused in the improved LAMP Constructs and methods described herein is bypolymerase chain reaction (PCR) amplification on selected nucleic acidtemplates with selected oligonucleotide primer pairs. For example,epithelial cells, endothelial cells, tumor cells, fibroblasts, activatedT cells, eosinophils, keratinocytes, astrocytes, microglial cells,thymic cortical epithelial cells, Schwann cells, retinal pigmentepithelial cells, myoblasts, vascular smooth muscle cells, chondrocytes,enterocytes, thyrocytes and kidney tubule cells can be used. These maybe primary cells recently explanted from a host and not extensivelypassaged in cell culture to form an established cell line, orestablished cell lines that are relatively homogeneous and capable ofproliferating for many generations or indefinitely.

Cells that are not professional APCs are isolated from any tissue of anautologous donor; a heterologous donor or a xenogeneic donor, where theyreside using a variety of known separation methods (Darling, AnimalCells: Culture and Media. J. Wiley, New York, 1994; Freshney, Culture ofAnimal Cells. Alan R. Liss, Inc., New York, 1987). Non-autologous cells,e.g., heterologous or xenogeneic cells, can be engineered ex vivo toexpress HLA class I and class II molecules that match known human HLAspecificities. These cells can then be introduced into a human subjectmatching the HLA specificity of the engineered cells. The cells arefurther engineered ex vivo to express one or more LAMP Constructsaccording to the invention.

The engineered cells are maintained in cell culture by standard cellculture methods (Darling, Animal Cells: Culture and Media”. J. Wiley,New York, 1994; Freshney, Culture of Animal Cells”. Alan R. Liss, Inc.,New York, 1987). Cell lines for use in the present invention areobtained from a variety of sources (e.g., ATCC Catalogue of Cell Lines &Hybridomas, American Type Culture Collection, 8th edition, 1995), or areproduced using standard methods (Freshney, Culture of ImmortalizedCells, Wiley-Liss, New York, 1996). Non-transformed cell lines arepreferred for use in human subjects.

In one aspect, CD34+ precursors that are differentiating under theinfluence of GM-CSF into dendritic cells are obtained from the body of asubject and nucleic acids encoding LAMP Constructs according to theinvention are introduced into the cells, which are then injected intothe subject. Utilizing the improved LAMP Constructs as described hereinwill enhance the association of peptides derived from a particularantigen with MHC class II molecules on the transduced antigen presentingcells, resulting in significantly more potent systemic T cell dependentimmune responses and/or antibody production. While the antigenpresenting cells transfected in this strategy are preferably autologouscells, any MHC class II cells that effectively present antigen in thehost may be used as described above.

Peptide Vaccines

Also within the scope of this invention are peptide vaccines encoded bythe improved LAMP Construct Preferably, the antigen is processed withinthe compartment/organelle (or subsequent compartment/organelle to whichit is delivered) to generate an epitope bound to an MHC class IImolecule capable of modulating an immune response.

The peptide vaccines encoded by the improved LAMP Constructs may alsomay be bound in a membranous structure to facilitate its administrationto the body of an organism. For example, the peptide vaccine encoded bythe improved LAMP Construct may be incorporated into liposomes, asdescribed in U.S. Pat. No. 4,448,765.

When a protein or polypeptide is to be used as an immunogen, it may beproduced by expression of any one or more of the improved LAMPConstructs described herein in a recombinant cell or it may be preparedby chemical synthesis. For example, the Merrifield technique (Journal ofAmerican Chemical Society, vol. 85, pp. 2149-2154, 1968), can be used.

Methods of Producing Antibodies Using LAMP Constructs

The improved LAMP Constructs as polynucleotides, the encoded proteins ofthe improved LAMP Constructs, and/or cells (such as antigen presentingcells which express the improved LAMP Constructs described herein) canbe used to generate antibodies by methods well known by the skilledartisan, such as, for example, methods described in the art. See, forinstance, Sutcliffe et al., supra; Wilson et al., supra; Chow et al.,Proc. Natl. Acad. Sci. USA 82:910-914 (1985); and Bittle et al., J. Gen.Virol. 66:2347-2354 (1985). If in vivo immunization is used, animals maybe immunized with a protein encoded by the improved LAMP Constructand/or a polynucleotide comprising the improved LAMP Constructcomprising an antigen as described herein. Priming with improved LAMPConstructs as polynucleotides, the encoded proteins of the improved LAMPConstructs, and/or cells (such as antigen presenting cells which expressthe improved LAMP Constructs described herein) followed by boosting withan antigen is a preferred embodiment of the invention. In furtherpreferred embodiments, priming with an improved LAMP Construct asdescribed herein followed by boosting with an antigen is specificallycontemplated and can be used to generate an even more robust immuneresponse, especially in view of antibody repertoire diversity and titer.

The improved LAMP Construct comprising the antigen may be injected intothe non-human vertebrate to raise antibodies. Preparation and injectionof LAMP Constructs into non-human vertebrates can be accomplishedaccording to principles of immunization of animals that are well knownto those skilled in the art.

The use of an improved LAMP Construct to effectively present the antigeninvolves, in one aspect, the antigen being processed by LAMP in AntigenPresenting Cells after endocytosis and fusion of the endosome with alysosome. The endosome then merges with an exocytic vesicle from theGolgi apparatus containing class II MHC molecules, to which theresultant peptides bind. The MHC-peptide complex then trafficks to theplasma membrane where the antigen is available for display to CD4+ Tcells.

Animals such as rabbits, rats, mice, llamas, camels, and/or cows can beimmunized with the improved LAMP Construct comprising an antigen and/ora polynucleotide encoding the improved LAMP Construct comprising anantigen. Additional animals suitable for immunization include, non-humanmammals, such as a rodent (e.g. a guinea pig, a hamster, a rat, amouse), murine (e.g. a mouse), canine (e.g. a dog), feline (e.g. a cat),equine (e.g. a horse), a primate, simian (e.g. a monkey or ape), amonkey (e.g. marmoset, baboon, rhesus macaque), an ape (e.g. gorilla,chimpanzee, orangutan, gibbon).

For instance, intraperitoneal and/or intradermal injection of emulsionscontaining about 100 micrograms of an improved LAMP Construct comprisingan antigen or carrier protein and Freund's adjuvant or any otheradjuvant known for stimulating an immune response may be used. Severalbooster injections (such as with the recombinant antigen protein) may beneeded, for instance, at intervals of about two weeks, to provide auseful titer of an anti-antigen antibody which can be detected, forexample, by ELISA assay using free antigen adsorbed, directly orindirectly (e.g., via a biotinylated AviTag), to a solid surface. Thetiter of anti-antigen antibodies in serum from an immunized animal maybe increased by selection of anti-antibodies, for instance, byadsorption to the antigen on a solid support and elution of the selectedantibodies according to methods well known in the art.

Alternatively, a polynucleotide encoding the improved LAMP Constructcomprising an antigen can also be directly introduced into animals. See,for example, U.S. Pat. Nos. 5,676,954; 6,875,748; 5,661,133; Sahin etal., Nat Rev Drug Discov, 2014 October; 13(10):759-80; Kariko et al.,Mol Ther, 2008 November; 16(11):1833-40; Kariko et al., Nucleic AcidRes, 2011, November; 39(21):e142; U.S. Pat. No. 6,511,832. In oneexample, an improved LAMP Construct comprising an antigen is directlyinjected into a non-human vertebrate. Injection into the animals canoccur via intramuscular, intradermal, intranasal, subcutaneous,intravenous, intratracheal, and intrathecal deliveries. Follow-onboosting with a recombinant antigen can also be include in generatingthe antibodies.

Additionally, antibodies generated by the disclosed methods can beaffinity matured using display technology, such as for example, phagedisplay, yeast display or ribosome display. In one example, single chainantibody molecules (“scFvs”) displayed on the surface of phage particlesare screened to identify those scFvs that immunospecifically bind to theantigen and/or the starting protein. The present invention encompassesboth scFvs and portions thereof that are identified toimmunospecifically bind to the antigen and/or the starting protein. SuchscFvs can routinely be “converted” to immunoglobulin molecules byinserting, for example, the nucleotide sequences encoding the VH and/orVL domains of the scFv into an expression vector containing the constantdomain sequences and engineered to direct the expression of theimmunoglobulin molecule.

Recombinant expression of the raised antibodies (including scFvs andother molecules comprising, or alternatively consisting of, antibodyfragments or variants thereof (e.g., a heavy or light chain of anantibody of the invention or a portion thereof or a single chainantibody of the invention)) using the improved LAMP Construct comprisingan antigen and/or a polynucleotide encoding the improved LAMP Constructcomprising an antigen of the invention, requires construction of anexpression vector(s) containing a polynucleotide that encodes theantibody or fragment or variant thereof. Once a polynucleotide encodingan antibody molecule (e.g., a whole antibody, a heavy or light chain ofan antibody, or variant or portion thereof (preferably, but notnecessarily, containing the heavy or light chain variable domain)), ofthe invention has been obtained, the vector(s) for the production of theantibody molecule may be produced by recombinant DNA technology usingtechniques well known in the art. Thus, methods for preparing anantibody by expressing a polynucleotide containing an antibody encodingnucleotide sequence are described herein. Methods which are well knownto those skilled in the art can be used to construct expression vectorscontaining the antibody coding sequences and appropriate transcriptionaland translational control signals. These methods include, for example,in vitro recombinant DNA techniques, synthetic techniques, and in vivogenetic recombination and are described herein. The invention, thus,provides replicable vectors comprising a nucleotide sequence encodingthe anti-antigen antibody obtained and isolated as described herein(e.g., a whole antibody, a heavy or light chain of an antibody, a heavyor light chain variable domain of an antibody, or a portion thereof, ora heavy or light chain CDR, a single chain Fv, or fragments or variantsthereof), operably linked to a promoter. Such vectors may include thenucleotide sequence encoding the constant region of the antibodymolecule (see, e.g., PCT Publication WO 86/05807; PCT Publication WO89/01036; and U.S. Pat. No. 5,122,464) and the variable domain of theantibody may be cloned into such a vector for expression of the entireheavy chain, the entire light chain, or both the entire heavy and lightchains.

The expression vector(s) can be transferred to a host cell byconventional techniques and the transfected cells are then cultured byconventional techniques to produce either the anti-antigen antibody.Thus, the invention includes host cells containing polynucleotide(s)encoding the anti-antigen antibody (e.g., whole antibody, a heavy orlight chain thereof, or portion thereof, or a single chain antibody ofthe invention, or a fragment or variant thereof), operably linked to aheterologous promoter. In preferred embodiments, for the expression ofentire antibody molecules, vectors encoding both the heavy and lightchains may be co-expressed in the host cell for expression of the entireimmunoglobulin molecule, as detailed below.

A variety of host-expression vector systems may be utilized to expressanti-antigen antibody. Such host-expression systems represent vehiclesby which the coding sequences of interest may be produced andsubsequently purified, but also represent cells which may, whentransformed or transfected, with the appropriate nucleotide codingsequences, express the anti-antigen antibody. These include, but are notlimited to, microorganisms such as bacteria (e.g., E. coli, B. subtilis)transformed with recombinant bacteriophage DNA, plasmid DNA or cosmidDNA expression vectors containing sequences; yeast (e.g., Saccharomyces,Pichia) transformed with recombinant yeast expression vectors containingcoding sequences; insect cell systems infected with recombinant virusexpression vectors (e.g., baculovirus) containing coding sequences;plant cell systems infected with recombinant virus expression vectors(e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) ortransformed with recombinant plasmid expression vectors (e.g., Tiplasmid) containing coding sequences; or mammalian cell systems (e.g.,COS, CHO, BHK, 293, 3T3 cells) harboring recombinant expressionconstructs containing promoters derived from the genome of mammaliancells (e.g., metallothionein promoter) or from mammalian viruses (e.g.,the adenovirus late promoter; the vaccinia virus 7.5K promoter).Preferably, bacterial cells such as Escherichia coli, and morepreferably, eukaryotic cells, are used for the expression of theanti-antigen antibody. For example, mammalian cells such as Chinesehamster ovary cells (CHO), in conjunction with a vector such as themajor intermediate early gene promoter element from humancytomegalovirus is an effective expression system (Foecking et al., Gene45:101 (1986); Cockett et al., Bio/Technology 8:2 (1990)).

In bacterial systems, a number of expression vectors may beadvantageously selected depending upon the intended use. For example,when a large quantity of a protein is to be produced (for eitherantibody production or encoded polypeptides of the improved LAMPConstruct), vectors which direct the expression of high levels of fusionprotein products that are readily purified may be desirable. Suchvectors include, but are not limited to, the E. coli expression vectorpUR278 (Ruther et al., EMBO 1. 2:1791 (1983)), in which the codingsequence may be ligated individually into the vector in frame with thelac Z coding region so that a fusion protein is produced; pIN vectors(Inouye & Inouye, Nucleic Acids Res. 13:3101-3109 (1985); Van Heeke &Schuster, J. Biol. Chem. 24:5503-5509 (1989)); and the like. pGEXvectors may also be used to express foreign polypeptides as fusionproteins with glutathione 5-transferase (GST). In general, such fusionproteins are soluble and can easily be purified from lysed cells byadsorption and binding to matrix glutathione agarose beads followed byelution in the presence of free glutathione. The pGEX vectors aredesigned to include thrombin or Factor Xa protease cleavage sites sothat the cloned target gene product can be released from the GST moiety.

In an insect system, Autographa californica nuclear polyhedrosis virus(AcNPV) may be used as a vector to express an anti-antigen antibody orthe encoded polypeptides of the improved LAMP Construct. The virus growsin Spodoptera frugiperda cells. Coding sequences may be clonedindividually into non-essential regions (for example, the polyhedringene) of the virus and placed under control of an AcNPV promoter (forexample, the polyhedrin promoter).

In mammalian host cells, a number of viral-based expression systems maybe utilized express an anti-antigen antibody or the encoded polypeptidesof the improved LAMP Construct. In cases where an adenovirus is used asan expression vector, the coding sequence of interest may be ligated toan adenovirus transcription/translation control complex, e.g., the latepromoter and tripartite leader sequence. This chimeric gene may then beinserted in the adenovirus genome by in vitro or in vivo recombination.

Insertion in a non-essential region of the viral genome (e.g., region E1or E3) will result in a recombinant virus that is viable and capable ofexpressing the anti-antigen antibody or the encoded polypeptides of theimproved LAMP Construct in infected hosts (e.g., see Logan & Shenk,Proc. Natl. Acad. Sci. USA 81:355-359 (1984)).

Specific initiation signals may also be required for efficienttranslation of inserted coding sequences. These signals include the ATGinitiation codon and adjacent sequences. Furthermore, the initiationcodon must be in phase with the reading frame of the desired codingsequence to ensure translation of the entire insert. These exogenoustranslational control signals and initiation codons can be of a varietyof origins, both natural and synthetic. The efficiency of expression maybe enhanced by the inclusion of appropriate transcription enhancerelements, transcription terminators, etc. (see, e.g., Bittner et al.,Methods in Enzymol. 153:51-544 (1987)).

In addition, a host cell strain may be chosen which modulates theexpression of the inserted sequences, or modifies and processes the geneproduct in the specific fashion desired. Such modifications (e.g.,glycosylation) and processing (e.g., cleavage) of protein products maybe important for the function of the protein. Different host cells havecharacteristic and specific mechanisms for the post-translationalprocessing and modification of proteins and gene products. Appropriatecell lines or host systems can be chosen to ensure the correctmodification and processing of the foreign protein expressed, to thisend, eukaryotic host cells which possess the cellular machinery forproper processing of the primary transcript, glycosylation, andphosphorylation of the gene product may be used. Such mammalian hostcells include, but are not limited to, CHO, VERY, BHK, Hela, COS, NSO,MDCK, 293, 3T3, W138, and in particular, breast cancer cell lines suchas, for example, BT483, Hs578T, HTB2, BT20 and T47D, and normal mammarygland cell line such as, for example, CRL7030 and HsS78Bst.

For long-term, high-yield production of recombinant proteins, stableexpression is preferred. For example, cell lines which stably expressthe express an anti-antigen antibody or the encoded polypeptides of theimproved LAMP Construct may be engineered. Rather than using expressionvectors which contain viral origins of replication, host cells can betransformed with a polynucleotide controlled by appropriate expressioncontrol elements (e.g., promoter, enhancer, sequences, transcriptionterminators, polyadenylation sites, etc.), and a selectable marker.Following the introduction of the foreign polynucleotide, engineeredcells may be allowed to grow for 1-2 days in an enriched media, and thenare switched to a selective media. The selectable marker in therecombinant plasmid confers resistance to the selection and allows cellsto stably integrate the plasmid into their chromosomes and grow to formfoci which in turn can be cloned and expanded into cell lines. Thismethod may advantageously be used to engineer cell lines which expressthe anti-antigen antibody or the encoded polypeptides of the improvedLAMP Construct.

A number of selection systems may be used, including but not limited to,the herpes simplex virus thymidine kinase (Wigler et al., Cell 11:223(1977)), hypoxanthineguanine phosphoribosyltransferase (Szybalska &Szybalski, Proc. Natl. Acad. Sci. USA 48:202 (1992)), and adeninephosphoribosyltransferase (Lowy et al., Cell 22:8 17 (1980)) genes canbe employed in tk-, hgprt- or aprt-cells, respectively. Also,antimetabolite resistance can be used as the basis of selection for thefollowing genes: dhfr, which confers resistance to methotrexate (Wigleret al., Natl. Acad. Sci. USA 77:357 (1980); O'Hare et al., Proc. Natl.Acad. Sci. USA 78:1527 (1981)); gpt, which confers resistance tomycophenolic acid (Mulligan & Berg, Proc. Natl. Acad. Sci. USA 78:2072(1981)); neo, which confers resistance to the aminoglycoside G-418(Goldspiel et al., Clinical Pharmacy, 12: 488-505 (1993); Wu and Wu,Biotherapy 3:87-95 (1991); Tolstoshev, Ann. Rev. Pharmacol. Toxicol.32:573-596 (1993); Mulligan, Science 260:926-932 (1993); and Morgan andAnderson, Ann. Rev. Biochem. 62: 191-217 (1993); TIB TECH 11(5):155-2 15(May; 1993)); and hygro, which confers resistance to hygromycin(Santerre et al., Gene 30:147 (1984)). Methods commonly known in the artof recombinant DNA technology may be routinely applied to select thedesired recombinant clone, and such methods are described, for example;in Ausubel et al. (eds.), Current Protocols in Molecular Biology, JohnWiley & Sons, N Y (1993); Kriegler, Gene Transfer and Expression, ALaboratory Manual, Stockton Press, N Y (1990); and in Chapters 12 and13, Dracopoli et al. (eds), Current Protocols in Human Genetics, JohnWiley & Sons, N Y (1994); Colberre-Garapin et al., J. Mol. Biol. 150:1(1981).

The expression levels of either an anti-antigen antibody or the encodedpolypeptides of the improved LAMP Construct can be increased by vectoramplification (for a review, see Bebbington and Hentschel, The Use OfVectors Based On Gene Amplification For The Expression Of Cloned GenesIn Mammalian Cells In DNA Cloning, Vol. 3. (Academic Press, New York,1987)). When a marker in the vector system expressing an anti-antigenantibody or the encoded polypeptides of the improved LAMP Construct isamplifiable, an increase in the level of inhibitor present in the hostcell culture will increase the number of copies of the marker gene.Since the amplified region is associated with the coding sequence,production of the anti-antigen antibody express or the encodedpolypeptides of the improved LAMP Construct will also increase (Crouseet al., Mol. Cell. Biol. 3:257 (1983)).

Other elements that can be included in vector sequences includeheterologous signal peptides (secretion signals), membrane anchoringsequences, introns, alternative splice sites, translation start and stopsignals, inteins, biotinylation sites and other sites promotingpost-translational modifications, purification tags, sequences encodingfusions to other proteins or peptides, separate coding regions separatedby internal ribosome reentry sites, sequences encoding “marker” proteinsthat, for example, confer selectability (e.g., antibiotic resistance) orsortability (e.g., fluorescence), modified nucleotides, and other knownpolynucleotide cis-acting features not limited to these examples.

The host cell may be co-transfected with two expression vectors of theinvention, for example, the first vector encoding a heavy chain derivedpolypeptide and the second vector encoding a light chain derivedpolypeptide. The two vectors may contain identical selectable markerswhich enable equal expression of heavy and light chain polypeptides.Alternatively, a single vector may be used which encodes, and is capableof expressing, both heavy and light chain polypeptides. In suchsituations, the light chain is preferably placed before the heavy chainto avoid an excess of toxic free heavy chain (Proudfoot, Nature 322:52(1986); Kohler, Proc. Natl. Acad. Sci. USA 77:2 197 (1980)). The codingsequences for the heavy and light chains may comprise cDNA or genomicDNA or synthetic DNA sequences.

Once an anti-antigen antibody or the encoded polypeptides of theimproved LAMP Construct has been produced by recombinant expression, itmay be purified by any method known in the art for purification of aprotein, for example, by chromatography (e.g., ion exchange, affinity(particularly by Protein A affinity and immunoaffinity for the specificantigen), and sizing column chromatography), centrifugation,differential solubility, or by any other standard technique for thepurification of proteins. Further, an anti-antigen antibody or theencoded polypeptides of the improved LAMP Construct may be fused toheterologous polypeptide sequences described herein or otherwise knownin the art to facilitate purification.

In one example, the anti-antigen antibody or the encoded polypeptides ofthe improved LAMP Construct may be fused with the constant domain ofimmunoglobulins (IgA, IgE, IgG, IgM), or portions thereof (CH1, CH2,CH3, or any combination thereof and portions thereof), or albumin(including but not limited to recombinant human albumin or fragments orvariants thereof (see, e.g., U.S. Pat. No. 5,876,969, issued Mar. 2,1999, EP Patent 0 413 622, and U.S. Pat. No. 5,766,883, issued Jun. 16,1998), resulting in chimeric polypeptides. Such fusion proteins mayfacilitate purification and may increase half-life in vivo. This hasbeen shown for chimeric proteins consisting of the first two domains ofthe human CD4-polypeptide and various domains of the constant regions ofthe heavy or light chains of mammalian immunoglobulins. See, e.g., EP394,827; Traunecker et al., Nature, 331:84-86 (1988). Enhanced deliveryof an antigen across the epithelial barrier to the immune system hasbeen demonstrated for antigens (e.g., insulin) conjugated to an FcRnbinding partner such as IgG or Fe fragments (see, e.g., PCT PublicationsWO 96/22024 and WO 99/04813). IgG Fusion proteins that have adisulfide-linked dimeric structure due to the IgG portion disulfidebonds have also been found to be more efficient in binding andneutralizing other molecules than monomeric polypeptides or fragmentsthereof alone. See, e.g., Fountoulakis et al., J. Biochem.,270:3958-3964 (1995). Nucleic acids encoding the anti-antigen antibodyor the encoded polypeptides of the improved LAMP Construct describedherein can also be recombined with a gene of interest as an epitope tag(e.g., the hemagglutinin (“HA”) tag or flag tag) to aid in detection andpurification of the expressed polypeptide. For example, a systemdescribed by Janknecht et al. allows for the ready purification ofnon-denatured fusion proteins expressed in human cell lines (Janknechtet al., 1991, Proc. Natl. Acad. Sci. USA 88:8972-897). In this system,the gene of interest is subcloned into a vaccinia recombination plasmidsuch that the open reading frame of the gene is translationally fused toan amino-terminal tag consisting of six histidine residues. The tagserves as a matrix-binding domain for the fusion protein. Extracts fromcells infected with the recombinant vaccinia virus are loaded ontoNi2+nitriloacetic acid-agarose column and histidine-tagged proteins canbe selectively eluted with imidazole-containing buffers.

Administration

Vaccine material according to this invention may contain the immunestimulatory improved LAMP Constructs described herein or may berecombinant microorganisms, or antigen presenting cells which expressthe immune stimulatory improved LAMP Constructs. Preparation of improvedLAMP Constructs containing vaccine material according to this inventionand administration of such improved LAMP Constructs for immunization ofindividuals are accomplished according to principles of immunizationthat are well known to those skilled in the art.

Large quantities of these materials may be obtained by culturingrecombinant or transformed cells containing replicons that express theimproved LAMP Constructs described herein. Culturing methods arewell-known to those skilled in the art and are taught in one or more ofthe documents cited above. The improved LAMP Construct vaccines aregenerally produced by culture of recombinant or transformed cells andformulated in a pharmacologically acceptable solution or suspension,which is usually a physiologically-compatible aqueous solution, or incoated tablets, tablets, capsules, suppositories or ampules, asdescribed in the art, for example in U.S. Pat. No. 4,446,128,incorporated herein by reference. Administration may be any suitableroute, including oral, rectal, intranasal or by injection whereinjection may be, for example, transdermal, subcutaneous, intramuscularor intravenous.

The improved LAMP Constructs are administered to a mammal in an amountsufficient to induce an immune response in the mammal. A minimumpreferred amount for administration is the amount required to elicitantibody formation to a concentration at least 4 times that whichexisted prior to administration. A typical initial dose foradministration would be 10-5000 micrograms when administeredintravenously, intramuscularly or subcutaneously, or 10⁵ to 10¹¹ plaqueforming units of a recombinant vector, although this amount may beadjusted by a clinician doing the administration as commonly occurs inthe administration of vaccines and other agents which induce immuneresponses. A single administration may usually be sufficient to induceimmunity, but multiple administrations may be carried out to assure orboost the response.

The improved LAMP Construct vaccines may be tested initially in anon-human mammal (e.g., a mouse or primate). For example, assays of theimmune responses of inoculated mice can be used to demonstrate greaterantibody, T cell proliferation, and cytotoxic T cell responses to theimproved LAMP Constructs than to wild type antigen. Improved LAMPConstructs can be evaluated in Rhesus monkeys to determine whether thevaccine formulation that is highly effective in mice will also elicit anappropriate monkey immune response. In one aspect, each monkey receivesa total of 5 mg DNA per immunization, delivered IM and divided between 2sites, with immunizations at day 0 and at weeks 4, 8, and 20, with anadditional doses optional. Antibody responses, ADCC, CD4+ and CD8+T-cell cytokine production, CD4+ and CD8+ T-cell antigen-specificcytokine staining can be measured to monitor immune responses to thevaccine.

Further description of suitable methods of formulation andadministration according to this invention may be found in U.S. Pat. No.4,454,116 (constructs), U.S. Pat. No. 4,681,762 (recombinant bacteria),and U.S. Pat. Nos. 4,592,002 and 4,920,209 (recombinant viruses).

Cancer Immunotherapy: Candidates for Prevention and Treatment

Candidates for cancer immunotherapy would be any patient with a cancertreated with either an improved LAMP Construct as described herein.Examples include patients with documented Epstein-Barr virus associatedlymphomas, patients with HPV associated cervical carcinomas, patientswith chronic HCV, or patients with a defined re-arrangement or mutationin an oncogene or tumor suppressor gene.

In preferred embodiments, cancers that can be treated using the vaccinesdescribed herein include, but are not limited to all stages ofprogression, including hyperplasia of an adenocarcinoma, sarcoma, skincancer, melanoma, bladder cancer, brain cancer, breast cancer, uterinecancer, ovarian cancer, prostate cancer, lung cancer (including, but notlimited to NSCLC, SCLC, squamous cell cancer), colorectal cancer, analcancer, rectal cancer, cervical cancer, liver cancer, head and neckcancer, oral cancer, salivary gland cancer, esophageal cancer, pancreascancer, pancreatic ductal adenocarcinoma (PDA), renal cancer, stomachcancer, kidney cancer, multiple myeloma or cerebral cancer.

It is envisioned that therapy with a vaccine composition comprising theimproved LAMP Constructs could be utilized at any period during thecourse of the individual's cancer, once it is identified. It is alsopossible that in high risk patients, vaccination in order to prevent thesubsequent emergence of a cancer.

Procedure for Therapy

In one embodiment, the improved LAMP Constructs could be injected intothe patient at any suitable time during the course of their malignancy.For example, the improved LAMP Constructs would be injected at a stagewhen the tumor burden was low. In an alternative embodiment in which theimproved LAMP Construct is introduced into the individual's antigenpresenting cells, precursors to the antigen presenting cells or matureantigen presenting cells are drawn either from the individual's bonemarrow or peripheral blood by vena puncture. These cells are establishedin culture followed by transduction with the improved LAMP Construct.Once transduction had occurred, these antigen presenting cells areinjected back into the patient.

In a particularly preferred embodiment, the invention provides a methodof treatment for a cancer patient having low tumor burden, such as earlyin the disease, after resection of a neoplastic tumor, or when theburden of tumor cells is otherwise reduced. In this method, a cellpopulation containing autologous stem cells capable of differentiationinto antigen presenting cells which will express MHC class II moleculesis obtained from the patient. These cells are cultured and transformedby introducing an improved LAMP Construct to deliver the antigen to beassociated with an MHC class II molecule either within thecompartment/organelle or within another compartment/organelle to whichthe antigen is delivered.

The transfected stem cell population is then reintroduced into thepatient, where the stem cells differentiate into antigen presentingcells which express MHC class II molecules complexed with Th epitopesfrom the antigen. The immune response to the antigen will be enhanced byenhanced stimulation of the helper T cell population.

More generally, in one embodiment, this invention provides a vaccinecomposition comprising the improved LAMP Construct for modulating animmune response in a mammal to an antigen (i.e., stimulating, enhancing,or reducing such a response).

Kits

The invention further comprises kits to facilitate performing themethods described herein. In one aspect, a kit comprises an improvedLAMP Construct as described herein and a cell for receiving the improvedLAMP Construct. The kit may additionally comprise one or more nucleicacids for engineering the cell into a professional APC. In one aspect,however, the cell is a professional APC. The cell may or may not expressco-stimulatory molecules. In a preferred aspect, when the cell does notexpress co-stimulatory molecules, the antigen encoded by the improvedLAMP Construct is an autoantigen. In another aspect, a panel of cells isprovided expressing different MHC molecules (e.g., known to be expressedin human beings). In a further aspect, the kit comprises reagents tofacilitate entry of the improved LAMP Constructs into a cell (e.g.,lipid-based formulations, viral packaging materials, cells, and thelike). In still a further aspect, one or more T cell lines specific forthe antigen encoded by the improved LAMP Construct is provided, toverify the ability of the improved LAMP Construct to elicit, modulate,or enhance an immune response.

Examples

The invention will now be further illustrated with reference to thefollowing examples. It will be appreciated that what follows is by wayof example only and that modifications to detail may be made while stillfalling within the scope of the invention.

Example 1—Construction of LAMP Constructs

The improved LAMP Constructs illustrated in FIG. 1 can be constructedusing standard molecular biology techniques well known to the skilledartisan. For example, plasmids comprising the polynucleotides can bedesigned to generate the different structures ILC-1 to ILC-6 shown inFIG. 1. The LAMP domains illustrated in FIG. 1 can be derived from theamino acid sequences shown in FIGS. 3-10. Preferably the LAMP domainsare derived from the human LAMP proteins shown in FIGS. 3-10. It isenvisioned that the corresponding domains can also be cloned from theorthologous sequences by identifying the equivalent domains whencompared to the human sequence. An antigen of interest (including one ormore antigens of interest) can be cloned into the described LAMPConstructs either individually or in combination.

Example 2—Immune Response Evaluation of Mice to LAMP Constructs

The ability of the improved LAMP Constructs as described in Example 1can be tested for their ability to modulate an immune response. Forexample, Female BALB/c mice can be immunized i.d with 50 ug of theimproved LAMP Constructs and 5 ug of GMCSF in 100 ul PBS using nanopasson day 0, 14 and 28. Experiment will then be terminated 4 weeks afterthe last dose.

Splenocytes (3×105/well) are stimulated with antigenic protein (10ug/ml) in T cell media (RPMI with 10% heat inactivated FBS, 1%penicillin/streptomycin, and 1×2-ME), supernatants are collected 72hafter. Supernatants are diluted (400 ul supernatant+200 ul T cell media)and cytokines are evaluated by ELISA. IL-10 or IL-4 production can bemeasured via ELISPOT assay.

Example 3—Improved Antigen Presentation Using LAMP Constructs

Survivin is the smallest member of the Inhibitor of Apoptosis (IAP)family of proteins, involved in inhibition of apoptosis and regulationof cell cycle. These functional attributes make Survivin a uniqueprotein exhibiting divergent functions i.e. regulating cellproliferation and cell death. Expression of Survivin in tumorscorrelates with not only inhibition of apoptosis and a decreased rate ofcell death, but also resistance to chemotherapy and aggressiveness oftumors [1-6]. Therefore, Survivin is an important target for cancervaccines and therapeutics [7-9]. Survivin has also been found to beprominently expressed on both human and embryonic stem cells and manysomatic stem cell types indicating its yet unexplored role in stem cellgeneration and maintenance.

Cancer is a heterogeneous group of diseases where abnormal cell growthwith potential to invade other body parts takes control of normalhomeostasis and becomes fatal if not timely and rightly treated.Immunotherapy specifically targets tumor cells thereby avoidingcollateral damage to non-tumor cells and inducing anti-tumor response.This anti-tumor response also has the potential to eradicate tumor atdistant sites in the body which may not be possible by surgicalresection. Induction or enhancement of anti-tumor immune response is aformidable challenge in cancer because tumor cells use multiple evasionstrategies and avoid being detected or eliminated by immune cells.

The aim of this project is to evaluate in vivo immune response of allnew generation of LAMP Constructs injected by I.D. in BALB/c mice.Specifically, mice were immunized with 50 pg of the tested constructsdefined in the legend of FIG. 1 by intradermal injection. No adjuvantswere added at this experiment. Six mice per group were administratedwith vaccines every 7 days with total three dose in one month. Immuneresponse was monitored 14 days after the last immunization.

The tested LAMP constructs were generated as described herein and thesequence of each tested construct is shown in FIG. 19. Survivin proteinwas purchased from MyBiosource (San Diego, Calif.). Survivin peptideswere from GenScript (Piscataway, N.J.). Anti-survivin and m-IgGk-BP-HRPwere bought from Santa Cruz Biotechnology (Dallas, Tex.), and mouseMonoclonal anti-LAMP-1/CD107a were from OriGene Technologies (Rockville,Md.). ELISPOT antibody pairs for IFNγ were from Biolegend. Fluorescentlycoupled CD3, CD4, CD8, CD44, CD62L, IFNγ, TNFα, granzyme B, CD69monoclonal antibodies and Zombie aqua fixable viability kit werepurchased from BioLegend (San Diego, Calif.). Goat anti-mouse IgG2a-HRPand goat anti-mouse IgG-HRP were purchased from Southern Biotechnologies(Birmingham, Ala.). Streptavidin-HRP was purchased from Thermo Fisher(Waltham, Mass.). SureBlue TMB microwell peroxidase substrate and TMBstop solution were purchased from KPL (Gaithersburg, Md.).

50 pg of each construct was used in a total volume of 100 ul per mouseper dose for Pharmajet. Mice were immunized with the vaccine by i.d.delivery on days 0, 7, and 14. Mice were bled on days 28 for serumcollection. Serum was collected and stored in −30° C. Spleens werecollected on day 28 at the termination of experiment and processed forELISPOT and FACS to evaluate survivin specific T cell responses.

Measurement of plasma survivin-specific total IgG by ELISA. The murineantibody response to survivin was assessed by indirect ELISA. ELISAplates (MaxiSorp) were coated with 2 pg/ml survivin (1-142) protein incarbonate-bicarbonate buffer overnight and then blocked with 2% BSA inPBS. Plasma samples were diluted 1:100 in blocking buffer. Samples weredetected with goat anti-mouse IgG-HRP (Southern Biotech, Birmingham,Ala.). Reaction was developed with SureBlue TMB Substrate and stoppedwith TMB Stop Solution from KPL (Gaithersburg, Md.). Plates were read(OD450) by using Epoch ELISA reader (BioTek, Winooski, Vt.).

Evaluation of antigen-specific T cell response. To assessantigen-specific T cell response in the vaccinated mice, splenocytesfrom vaccinated mice were evaluated for antigen-specific IFNγ productionby Enzyme-linked immunospot (ELISPOT). For ELISPOT assays, 96-wellnitrocellulose plates (Millipore), were coated overnight at 4° C. with100 μl/well of capture monoclonal antibody in PBS. The plates werewashed three times with 200 μl/well PBS and blocked with 200 μl/well Tcell media for at least 2 hrs at room temperature. Splenocytes wereplated at 3×10⁵ cells/well and co-cultured with 2 μg/ml pooled peptidesof Survivin (Table 1) or concavalin A (0.125 pg/ml) or medium alone in atotal volume of 200 μl/well T cell media (RPMI-1640 with L-Glutamine andHEPES (ATCC), 1% penicillin, 1% streptomycin, and 5×10⁻⁵M β-ME) at 3×10⁵cells/well for 48h at 37° C. in 5% CO₂. The plates were washed two timeswith 200 μl/well PBS and two times with 200 μl/well PBS-T (0.05%Tween/PBS). Diluted detection antibodies (50 μl/well in PBS-T/0.5% BSA)were added and plates were incubated for 2 hrs with shaking at roomtemperature. Plates were washed four times with PBS.Streptavidin-alkaline phosphatase diluted in PBS (50 μl/well) were addedand incubated for 2 h. Plates were washed with PBS four times anddeveloped with 50 l/well of 3-Amino-9-Ethylcarbazole (AEC, BDBioscience) substrate for 10 min. Color development was stopped bywashing under running tap water. After drying 72h at room temperature indark, colored spots were counted using an AID ELISPOT High-ResolutionReader System and AID ELISPOT Software version 3.5 (AutoimmunDiagnostika GmbH).

TABLE 1 Pooled peptides from Genscript Pooled P1 Sur1-15, Sur11-25, Sur21-35, Sur31-45, sur 41-55 Pooled P2 Sur51-65, sur61-75, sur71-85,sur81-95 Pooled P3 Sur91-105, sur 101-115, sur111-125, sur121-135,sur131-142 Pooled P4 Sur31-45, sur41-55 and sur51-65

Western blots. 293T cells were transfected with the tested constructsusing lipofectamine 2000 reagents (Invitrogen). Transfected cells werewashed with PBS and suspended in 200 μl of RIPA lysis buffer with haltproteinase inhibitors (Thermo Scientific, Waltham, Mass.). Lysates werecentrifuges (700 g for 15 minutes at 4° C.), followed by measurement ofprotein concentration in the clarified supernatants using Pierce BCAprotein Assay kit (ThermoFisher Scientific, Waltham, Mass.). 10 pg ofprotein was electrophoresed in pre-cast (4-20%) SDS-PAGE gels (BioRad,Hercules, Calif.), and transferred onto nitrocellulose membranes(BioRad) and immunoblotted with mAbs to hLAMP. Membranes were blockedwith Detection™ block buffer (KPL) and probed with rabbit anti-humanLAMP (Sino Biological Inc., Beijing, China) or anti-survivin antibodyand goat anti-rabbit-HRP antibody, and then developed with TMB (KPL).

Flow cytometry. Cells were first labelled with Zombie aqua fixableviability dye in PBS (1:500 dilution), followed by surface antibodies(1:100 dilution) in staining buffer (4% FBS, 2% rat serum, 2% mouseserum in PBS). For intracellular staining cells were stained with Zombieaqua, followed by surface staining, fixation with 4% paraformaldehyde,and stained with intracellular antibody in permeabilization buffer (PBSwith 1% FCS 0.1% saponin). Samples were analyzed on a CytoFlex flowcytometer (Beckman Coulter) and analyzed using Kaluza software (BeckmanCoulter).

Statistics. Two-Way ANOVA test was performed using GraphPad Prism 6.0software or R file to evaluate the statistical significance. Eachmouse's RPMI result was deducted from the results of the antigenactivation.

Study Design.

18-ONC-019 Survivin Pharmajet validation in Balb/c mice (serum) T/W # INPJ = yes DNA = yes Group Treatment Concentration Dose Route Mice Vol.Mice ID Eartag D-0 D-7 D-14 D-28 Feb. 16, 2018 Feb. 26, Mar. 5, Mar. 12,Mar. 26, 2018 A Control Vector 2.52 mg/ml 50 ug Pharamajet 6 100 ul7896-7901 Eartag/ 2018 2018 2018 Harvest B Survivin + LAMP 3.4 mg/ml 50ug Pharamajet 6 100 ul 7902-7907 Pre few 1^(st) 2nd 3^(rd) spleen and CSurvivin 5.88 mg/ml 50 ug Pharamajet 6 100 ul 7908-7913 per groupImmuni- Immuni- Immuni- serum preluminal LAMP pool zation zation zationD LAMP-luminal- 2 mg/ml 50 ug Pharamajet 6 100 ul 7914-7919 D1-survivinE Survivin-LAMP- 2 mg/ml 50 ug Pharamajet 6 100 ul 7997-8002 luminaldomain1 F LAMP-hinge- 2 mg/ml 50 ug Pharamajet 6 100 ul 8003-8008survivin

FIG. 14: Validation of the plasmids: 293T cells were transfected withthe plasmids for 3 days. Transfected cells were lysed, and thenelectrophoresed in pre-cast SDS-PAGE gel. The proteins were transferredto nitrocellulose membranes and immunoblotted with mAbs to human LAMP(OriGene, #TA337108) or survivin Santa Cruz #17779). Molecular weight ofLAMP=100 KD, Survivin=16 KD. FIG. 13 shows that all tested LAMPconstructs produced appropriately sized protein.

FIGS. 15 and 16: Tested LAMP Constructs induce Th1 effector T cellsproducing IFNγ. Female BALB/c mice were immunized i.d with 50 pg of theindicated constructs in 100 μl PBS via Pharmajet device on day 0, 7 and14. Experiment was terminated 14 days after the last dose. Splenocytes(3×10⁵/well) were stimulated with survivin pooled peptides (4 pg/ml) inT cell media (RPMI with 10% heat inactivated FBS, 1%penicillin/streptomycin, and 1×β-ME), for 48 h. A. IFNγ production byspots. B. IFNγ production induced by all pooled peptides (bar figurefrom A). n=6 per group. Two way ANOVA (R file) was used for statisticalanalysis. FIG. 14 shows that all tested LAMP constructs induced a robustT cell response as shown by IFNγ production.

We unexpectedly found that after 3 dose of the improved LAMP Constructs(one week apart), a robust Th1 type response elicited by tested LAMPConstructs, especially ILC-4 where the hinge sequence was replaced bysurvivin gene. More interestingly, improved LAMP Construct ILC-4 appearsto recognize the survivin epitopes from N-terminal to C-terminal, andinduce T cell response against human survivin peptide sequence which is100% identical to the mouse. We also found longer (72 hrs) stimulationof frozen-thawed splenocyte cells with survivin peptides, ILC-4 showedsignificant higher IFNγ production than the first generation ofLAMP-survivin (see FIG. 19). Specifically, FIG. 16 shows that the allimproved LAMP Constructs tested showed higher T cell response with ILC-4having the best activity as this constructed elicited a significantlyhigher T cell response against all survivin peptides pools. Moreover,contrary to what was known in the art, removal of the second homologydomain of the luminal domain created an improved LAMP construct thatelicited a more robust immune response as compared to the complete LAMPconstruct (see, results for ILC-2 and ILC-3). Frozen splenocytes(4×105/well) were stimulated with pooled peptides 4 (4 μg/ml) in T cellmedia (RPMI with 10% heat inactivated FBS, 1% penicillin/streptomycin,and 1×β-ME), for 48 h. n=6 per group. Two way ANOVA was used forstatistical analysis. *p<0.05, p<0.01, ***p<0.005, ****p<0.0001

FIG. 17. CD4 T cells are the major source of IFNγ producing cells.Female BALB/c mice were immunized i.d with 50 pg of the indicatedvaccines in 100 μl PBS via Pharmajet device on day 0, 7 and 14.Experiment was terminated 14 days after the last dose. Splenocytes(1×10⁶/well) were stimulated with pooled peptides 1 (4 μg/ml) in T cellmedia (RPMI with 10% heat inactivated FBS, 1% penicillin/streptomycin,and 1×β-ME) over night, followed by adding monesin and brefeldin A andculturing for additional Sh. Cells were harvested and stained by Zombie,surface marker, and intracellular staining according to ITI stainingprotocol. Cells are gated on memory CD4 T cells (CD4+CD44+CD62L−) or CD8T cells (CD8+CD44+CD62L−). Data is representative of one mouse in eachgroup. While there is an increase in CD8 effector memory cells invaccinated mice with the various constructs, IFNγ production is morepronounced in the CD4 T cell population.

FIG. 18: Improved LAMP Constructs produced stronger survivin-specifictotal IgG response in BALB/c mice. Female BALB/c mice were immunized i.dwith 50 μg of the indicated vaccines in 100 μl PBS via Pharmajet deviceon day 0, 7 and 14. Experiment was terminated 14 days after the lastdose. Mice were bleed on days 28. Serum was separated and stored in −30°C. Total IgG and IgG2a were determined in serum by ELISA. Briefly, ELISAplates were coated with 2 μg/ml survivin (1-142aa), blocked with PBS/2%BSA, serum (1:100 dilution in blocking buffer) were evaluated byHRP-conjugated goat anti mouse IgG (1:6000) and IgG2a (1:11000). n=6mice per group. **p<0.01, ***p<0.005, ****p<0.0001. Importantly andcontrary to what was known in the art, FIG. 18 shows that fragments ofthe luminal domain worked better than use of the complete luminal domain(i.e., compare complete LAMP construct with constructs ILC-2 and IL-3).Moreover and unexpectedly, insertion of the antigen between the twohomology domains of the luminal domain generated the strongest antibodyresponse (see, ILC-4).

REFERENCES RELIED ON IN THIS SECTION

-   1. Kami K, Doi R, Koizumi M, Toyoda E, Mori T, Ito D, et al.    Survivin expression is a prognostic marker in pancreatic cancer    patients. Surgery. 2004; 136(2):443-8. doi:    10.1016/j.surg.2004.05.023. PubMed PMID: 15300213.-   2. Zhang S Q, Qiang S Y, Yang W B, Jiang J T, Ji Z Z. [Expression of    survivin in different stages of carcinogenesis and progression of    breast cancer]. Ai Zheng. 2004; 23(6):697-700. PubMed PMID:    15191674.-   3. Zhang X, Zhong L, Hu K, Li Q. [Expression of survivin and its    correlation with apoptosis in non-small cell lung cancer]. Zhongguo    Fei Ai Za Zhi. 2004; 7(2):138-41. doi:    10.3779/j.issn.1009-3419.2004.02.14. PubMed PMID: 21215009.-   4. Kishi H, Igawa M, Kikuno N, Yoshino T, Urakami S, Shiina H.    Expression of the survivin gene in prostate cancer: correlation with    clinicopathological characteristics, proliferative activity and    apoptosis. J Urol. 2004; 171(5):1855-60. doi:    10.1097/01.ju.0000120317.88372.03. PubMed PMID: 15076293.-   5. Asanuma K, Tsuji N, Endoh T, Yagihashi A, Watanabe N. Survivin    enhances Fas ligand expression via up-regulation of specificity    protein 1-mediated gene transcription in colon cancer cells. J    Immunol. 2004; 172(6):3922-9. PubMed PMID: 15004200.-   6. Miyachi K, Sasaki K, Onodera S, Taguchi T, Nagamachi M, Kaneko H,    et al. Correlation between survivin mRNA expression and lymph node    metastasis in gastric cancer. Gastric Cancer. 2003; 6(4):217-24.    doi: 10.1007/s10120-003-0255-2. PubMed PMID: 14716515.-   7. Badana A K, Chintala M, Gavara M M, Naik S, Kumari S, Kappala V    R, et al. Lipid rafts disruption induces apoptosis by attenuating    expression of LRP6 and survivin in triple negative breast cancer.    Biomed Pharmacother. 2017; 97:359-68. doi:    10.1016/j.biopha.2017.10.045. PubMed PMID: 29091885.-   8. Cai J P, Wang Y D, Zhang X, Xue H Z. [Expression of P16 and    survivin in liver cancer and their clinical significance]. Zhonghua    Gan Zang Bing Za Zhi. 2017; 25(10):778-80. doi:    10.3760/cma.j.issn.1007-3418.2017.10.013. PubMed PMID: 29108210.-   9. Cho H J, Kim H R, Park Y S, Kim Y H, Kim D K, Park S I.    Prognostic value of survivin expression in stage III non-small cell    lung cancer patients treated with platinum-based therapy. Surg    Oncol. 2015; 24(4):329-34. doi: 10.1016/j.suronc.2015.09.001. PubMed    PMID: 26690822.-   10. Godinho R M, Matassoli F L, Lucas C G, Rigato P O, Goncalves J    L, Sato M N, et al. Regulation of HIV-Gag expression and targeting    to the endolysosomal/secretory pathway by the luminal domain of    lysosomal-associated membrane protein (LAMP-1) enhance Gag-specific    immune response. PLoS One. 2014; 9(6):e99887. doi:    10.1371/journal.pone.0099887. PubMed PMID: 24932692; PubMed Central    PMCID: PMCPMC4059647.

Example 4: Therapeutic Treatment of LAMP Constructs

Female BALB/c mice can be inoculated s.c with syngeneic 7000 4T1 mammarycarcinoma cells on day 0. Vaccine 50 ug and 5 ug of GMCSF in 100 ul PBSis given i.d using nanopass once the tumors are palpable. Primary tumorsare measured with a caliper and tumor volume is calculated using theformula p/6 (length×width)3/2. Average tumor volume as a function ofdays after tumor inoculation can be measured. A Kaplan-Meier plot can beused to show overall survival at the point of termination.

Example 5—Prime/Boost Protocol

Herpesvirus entry mediator (HVEM), also known as tumor necrosis factorreceptor superfamily member 14 (TNFRSF14) or CD270, is a human cellsurface receptor of the TNF-receptor superfamily. In recent years, HVEMhas been found highly expressed on hematopoietic cells and a variety ofparenchymal cells, such as breast, melanoma, colorectal, and ovariancancer cells, as well as gut epithelium. HVEM is a bidirectionalprotein, either inhibiting or stimulating T cells, through binding toBTLA or LIGHT (TNFSF14).

We generated a DNA vaccine encoding HVEM-LAMP to generate an antibodywhich could block the inhibitory function of HVEM for tumor therapeuticapplications. We hypothesized that LAMP will promote the antibodyresponse by enhancing the affinity of HVEM specific antibodies and/orexpanding the repertoire of B cell epitopes in the HVEM protein. In thisstudy, we compared the immunogenicity of HVEM encoding plasmid with andwithout LAMP. The HVEM sequence:

HVEM amino acids 39-202 (SEQ ID NO: 114)LPSCKEDEYPVGSECCPKCSPGYRVKEACGELTGTVCEPCPPGTYIAHLNGLSKCLQCQMCDPAMGLRASRNCSRTENAVCGCSPGHFCIVQDGDHCAACRAYATSSPGQRVQKGGTESQDTLCQNCPPGTFSPNGTLEEC QHQTKCSWLVTKAGAGTSSSHWV

Plasmids encoding HVEM-LAMP and HVEM and recombinant HVEM protein weredesigned by ITI and produced by NTC (Lincoln, Nebr.). Polynucleotidesencoding the following HVEM sequence was cloned into the improved LAMPConstructs described herein:

Goat anti-mouse IgG-HRP was purchased from Southern Biotechnologies(Birmingham, Ala.). SureBlue TMB microwell peroxidase substrate and TMBstop solution were purchased from KPL (Gaithersburg, Md.). ELISPOTplates were ordered from EMD Millipore (Billerica, Mass., Cat. No.MAIPS4510). IFN-γ antibody pair used in ELISPOT was purchased fromBioLegend (San Diego, Calif.) and clones AN18 and R46A2 were used ascoating and detection, respectively. Streptavidin-HRP and AEC substratewere purchased from BD Biosciences (San Jose, Calif.).

Six to eight week old female Balb/c mice were purchased from HarlanLaboratories (Frederick, Mass.) and maintained at animal facility inImmunomic Therapeutics, Inc. (Rockville, Mass.). Mice (n=6) were treatedwith 10 μg/dose of HVEM-LAMP, HVEM, or LAMP vector control by Ichorelectroporation IM delivery at days 0, 7, and 14. On day 35, mice wereboosted with 5 μg HVEM protein in the presence of Alum by i.p.injection. On day 28 and 49, mice were bled and sera were isolated forantibody detection. Mice were sacrificed on day 56 and splenocytes weretested for IFN-γ production by ELISPOT.

ELISA procedure was followed by Su et al., J of Immunol Res; (10):1-15(2016). Plates were coated with 5 μg/ml HVEM protein. Data were analyzedby using Microsoft Excel and Prism 6 software.

The primary aim of this study was to compare the antibody profilesbetween HVEM-LAMP and HVEM. On day 28, HVEM-LAMP vaccinated miceproduced significant higher level of HVEM specific IgG antibody thanthat of the HVEM group (FIG. 11). After a protein boost, the HVEMspecific antibody was increased about 1000-fold in HVEM immunized miceand the mean titer was changed from 100 to 108000. This result indicatesthat the immune memory was induced by the HVEM DNA plasmid. AlthoughHVEM DNA alone only induced a minimal antibody response, protein boostrapidly recalled the immune memory. On the other hand, HVEM-LAMP groupagain exhibited a significant higher titer than the HVEM and LAMPgroups, the mean titer is 5 folds of the HVEM group, indicating thepower of LAMP in enhancing antibody response (FIG. 12).

Additionally serum samples (Day 49) from HVEM+LAMP or HVEM aloneimmunized/HVEM protein boosted mice were pooled and tested for peptidemapping. Twelve peptides were found to be bound to the pooled serum(mouse IgG reaction) and seven of the twelve peptides showed strongbinding affinity. HVEM+LAMP alters the binding affinity of peptides 17.24, 25, and 28 as compared to HVEM alone as shown in FIG. 13. Thesechanges may have physiological effects in protecting tumor growth.

In conclusion, data from this study suggest that two constructs wereexpressed in vivo and LAMP significantly improved the humoral immuneresponse.

Example 6: Production of an Antibody from a Polypeptide

Anti-antigen antibodies can be prepared by a variety of standard methodsof raising antibodies using animal injection. (See, Current Protocols,Chapter 2.) For example, cells expressing an improved LAMP Constructcomprising an antigen described herein is administered to a non-humanvertebrate to induce the production of sera containing polyclonalantibodies. In a preferred method, a preparation of the LAMP/antigenprotein is prepared and purified to render it substantially free ofnatural contaminants. Such a preparation is then introduced into thenon-human vertebrate to produce polyclonal antisera of greater specificactivity.

In the most preferred method, the anti-antigen antibodies of the presentinvention are monoclonal antibodies (or protein binding fragmentsthereof). Such monoclonal antibodies can be prepared using hybridomatechnology. (Kohler et al., Nature 256:495 (1975); Kohler et al., Eur.J. Immunol. 6:511 (1976); Kohler et al., Eur. J. Immunol. 6:292 (1976);Hammerling et al., in: Monoclonal Antibodies and T-Cell Hybridomas,Elsevier, N.Y., pp. 563-681 (1981).) In general, such procedures involveimmunizing a non-human vertebrate animal (preferably a rabbit, mouse,cow, camel, llama) with an improved LAMP Construct comprising anantigen, the encoded polypeptide of an improved LAMP Constructcomprising an antigen or, more preferably, with an improved LAMPConstruct-expressing cell. Such cells may be cultured in any suitabletissue culture medium; however, it is preferable to culture cells inEarle's modified Eagle's medium supplemented with 10% fetal bovine serum(inactivated at about 56 degrees C.), and supplemented with about 10 g/lof nonessential amino acids, about 1,000 U/ml of penicillin, and about100 ug/ml of streptomycin.

The splenocytes of such non-human vertebrate host (e.g, mice) areextracted and fused with a suitable myeloma cell line. Any suitablemyeloma cell line may be employed in accordance with the presentinvention; however, it is preferable to employ the parent myeloma cellline (SP20), available from the ATCC™. After fusion, the resultinghybridoma cells are selectively maintained in HAT medium, and thencloned by limiting dilution as described by Wands et al.(Gastroenterology 80:225-232 (1981).) The hybridoma cells obtainedthrough such a selection are then assayed to identify clones whichsecrete antibodies capable of binding the antigen.

It will be appreciated that Fab and F(ab′)2 and other fragments of theanti-antigen antibodies may be used according to the methods disclosedherein. Such fragments are typically produced by proteolytic cleavage,using enzymes such as papain (to produce Fab fragments) or pepsin (toproduce F(ab′)2 fragments). Alternatively, secreted protein-bindingfragments can be produced through the application of recombinant DNAtechnology or through synthetic chemistry.

For in vivo use of antibodies in humans, it may be preferable to use“humanized” chimeric monoclonal antibodies. Such antibodies can beproduced using genetic constructs derived from hybridoma cells producingthe monoclonal antibodies described above. Methods for producingchimeric antibodies are known in the art. (See, for review, Morrison,Science 229:1202 (1985); Oi et al., BioTechniques 4:214 (1986); Cabillyet al., U.S. Pat. No. 4,816,567; Taniguchi et al., EP 171496; Morrisonet al., EP 173494; Neuberger et al., WO 8601533; Robinson et al., WO8702671; Boulianne et al., Nature 312:643 (1984); Neuberger et al.,Nature 314:268 (1985).)

Example 7: Use of Polynucleotides to Generate Polyclonal and MonoclonalAntibodies

Methods of directly injecting polynucleotides into animals are welldescribed in the art. See, for example, U.S. Pat. Nos. 5,676,954;6,875,748; 5,661,133. For example, a polynucleotide encoding an improvedLAMP Construct comprising an antigen can be injected into the quadricepsmuscles of restrained awake mice (female 6-12 week old BALB/c or Nude,nu/nu, from Harlan Sprague Dawley, Indianapolis, Ind.). In oneembodiment, 50 μg of a polynucleotide in 50 μl solution using adisposable sterile, plastic insulin syringe and 28G W needle(Becton-Dickinson, Franklin Lakes, N.J., Cat. No. 329430) fitted with aplastic collar cut from a micropipette tip can be used to inject themice, as described in Hartikka, J., et al., Hum. Gene Ther. 7:1205-1217(1996)).

Alternatively, 6-week old Sprague Dawley female mice (body weight 20-25grams) can be given 5000 ppm ZnOSO4 in their drinking water beginning 24hours prior to injection. This amount of zinc has been shown to be ableto activate the metallothionein promoter. Each mouse is then injectedintravenously through a tail vein puncture with a 25 gauge needle with30 μg of a polynucleotide encoding an improved LAMP Construct comprisingan antigen complexed with 150 μg liposome (Lipofection™) in a totalvolume of 30 μl. Animal care should be maintained throughout the studyand should be performed in compliance with the “Guide for the Use andCare of Laboratory Animals”, Institute of Laboratory Animal Resources,Commission on Life Sciences, National Research Council, National AcademyPress.

After the injected polynucleotide encoding the improved LAMP Constructcomprising an antigen is delivered into the cells in the animal, theantigen is delivered to the endosome/lysosome, processed and presentedto the immune system. The improved LAMP Construct comprising an antigencan then stimulate the production of antibodies specific to the antigen.These antibodies can be isolated and used as a polyclonal mixture orfurther isolated into single species or monoclonals. The process of theimmune response and production of antibodies against foreign antigens invivo are well known in the art.

In a third animal model, Balb/c 3T3 A31 cells are transfected byelectroporation with a polynucleotide encoding an improved LAMPConstruct comprising an antigen. G418 resistant clones expressing LAMPConstruct comprising an antigen are identified by their ability to bindhuman RBC. To generate polyclonal antibodies, Balb/c mice are immunizedtwice intraperitoneally, at an interval of 14 days, with 10⁷ cellscomprising the improved LAMP Construct comprising an antigen. After afinal boost, the immune serum is collected, IgG is purified by protein GSepharose and passed over an antigen column prepared by coupling 1.0 mgpurified antigen to cyanogen bromide activated Sepharose CL-4B. BoundIgG can be eluted with 0.1 M glycine buffer pH 2.5 and neutralized with0.1 volumes of 0.1 M Tris pH 8.0. To generate a monoclonal antibody(mAb), Balb/c mice are immunized with LAMP Construct comprising anantigen and hybridomas are generated by fusing immune spleen cells withthe SP2 myeloma following standard methods (28). A positive wellreacting specifically with an antigen can be identified by enzyme-linkedimmunosorbent assays as described in the art. The hybridoma is clonedthree times by limiting dilution to produce an antibody.

Example 8: Immunization of an Improved LAMP Construct Comprising anAntigen

Methods of raising antibodies in mammals are well known in the art. Inone example, polyclonal antiserum against LAMP Construct comprising anantigen is raised by immunization of pathogen free rabbits with a totalof 500 μg an improved LAMP Construct comprising an antigen over a periodof two months. For example, the improved LAMP Construct comprising anantigen can be dissolved in PBS and emulsified with an equal volume ofFreund's adjuvant. After the final booster, the serum of the rabbits canbe separated to determine the titer of the polyclonal antiserum.

In an additional animal model, groups of 5 mice (C57BL/6J; Jackson Labs)can be subcutaneously immunized with 5 μg of endotoxin-free LAMPConstruct comprising an antigen emulsified in alum. Three weeks later,mice are bled and the presence of anti-antigen specific antibodies canbe determined by titering the seras by ELISA (direct binding ofantibodies in sera to wild type BPTI or APP-KI coated, directly orindirectly (via a biotinylated tag and streptavidin), on the wells).

To obtain monoclonal antibodies, 4-6 week old Balb/c mice can beimmunized with an improved LAMP Construct comprising an antigen (forexample 4 times with 2 week intervals with 10-100 μg/injection dissolvedin Freunds complete adjuvant for the first injection, and Freund'sincomplete adjuvant for subsequent immunizations). Splenocytes areisolated and fused with a fusion cell line such as Sp2/0 myeloma cells,followed by limiting dilution. Growing clones are screened using forexample an enzyme-linked immunosorbant assay (ELISA). 96 cells platesare coated with an improved LAMP Construct comprising an antigen or witha control protein. The culture supernatant is added, followed by washingand addition of a labeled anti-mouse antibody for detection. Afterlimited dilution cloning of the anti-antigen antibody producing stablehybridomas are obtained. From each cell, supernatant is collected and byaffinity chromatography using protein A sepharose columns monoclonalantibodies can be purified.

Variations, modifications, and other implementations of what isdescribed herein will occur to those of ordinary skill in the artwithout departing from the spirit and scope of the invention and theclaims. All of the patents, patent applications, internationalapplications, and references identified are expressly incorporatedherein by reference in their entireties.

1.-23. (canceled)
 24. A human lysosomal associated membrane protein 1(“human LAMP-1”) Construct comprising two homology domains of a luminaldomain of human LAMP-1 protein, and comprising an antigenic domainheterologous to the human LAMP-1 protein, wherein the antigenic domainis placed between the two homology domains.
 25. The human LAMP-1Construct of claim 24, wherein the two homology domains comprise humanLAMP-1 Homology Domain 1 and human LAMP-1 Homology Domain
 2. 26. Thehuman LAMP-1 Construct of claim 25, wherein the human LAMP-1 HomologyDomain 1 comprises the amino acid sequence of residues 29-194 of SEQ IDNO:
 1. 27. The human LAMP-1 Construct of claim 25, wherein the humanLAMP-1 Homology Domain 2 comprises the amino acid sequence of residues228-381 of SEQ ID NO:
 1. 28. The human LAMP-1 Construct of claim 25,wherein the human LAMP-1 Homology Domain 1 comprises the amino acidsequence of residues 29-194 of SEQ ID NO: 1, and wherein the humanLAMP-1 Homology Domain 2 comprises the amino acid sequence of residues228-381 of SEQ ID NO:
 1. 29. The human LAMP-1 Construct of claim 24,wherein the Construct comprises a linker between at least one of the twohomology domains and the antigenic domain.
 30. The human LAMP-1Construct of claim 29, wherein the linker comprises an amino acidsequence of GPGPG or PMGLP.
 31. The human LAMP-1 Construct of claim 24,wherein the Construct further comprises a Transmembrane Domain of a LAMPProtein.
 32. The human LAMP-1 Construct of claim 31, wherein theTransmembrane Domain comprises residues 383 to 405 of SEQ ID NO:
 1. 33.The human LAMP-1 Construct of claim 31, wherein the Construct furthercomprises a Cytoplasmic Tail of a LAMP protein.
 34. The human LAMP-1Construct of claim 33, wherein the Cytoplasmic Tail comprises residues406-417 of SEQ ID NO:
 1. 35. The human LAMP-1 Construct of any of claim24, wherein the Construct further comprises a signal sequence.
 36. Thehuman LAMP-1 Construct of claim 35, wherein the signal sequence isderived from a LAMP Protein.
 37. A polynucleotide encoding the humanLAMP-1 Construct of claim
 24. 38. The polynucleotide of claim 37,wherein the polynucleotide is DNA.
 39. The polynucleotide of claim 37,wherein the polynucleotide is mRNA.
 40. A host cell comprising thepolynucleotide of claim
 37. 41. A composition comprising the humanLAMP-1 Construct of claim
 24. 42. A composition comprising thepolynucleotide of claim
 37. 43. A composition comprising the host cellof claim
 40. 44. A method of treating a subject having a disease or adisorder, wherein the method comprises administering to a subject inneed thereof the human LAMP-1 Construct of claim 24 in an amountsufficient to reduce or treat the disease or disorder.
 45. The method ofclaim 44, wherein the method comprises a priming step and at least oneboosting step.
 46. The method of claim 45, wherein the human LAMP-1Construct is used in the priming step.
 47. The method of claim 45,wherein the boosting step comprises administration of an antigen, thehuman LAMP-1 Construct, the polypeptide encoded by a human LAMP-1Construct, or a cell comprising the human LAMP-1 Construct.
 48. Themethod of claim 45, wherein the antigen used to prime is the same thatis used to boost.
 49. The method of claim 45, wherein the antigen usedto prime is derived from the same protein as a second antigen used toboost.
 50. The method of claim 45, wherein more than one antigen is usedto prime and/or boost.